Claudia Rangel Escareño, PhD

Adjunct Faculty Institute of Mathematical Sciences, Claremont Graduate University. Claremont California

P.I. Computational and Integrative Genomics, National Institute of Genomic Medicine, Mexico
Office Phone: +52-55-5350-1976
email: crangel(at)inmegen(dot)gob(dot)mx

 

Publications

Olvera-García G, Aguilar-García T, Gutiérrez-Jasso F, Imaz-Rosshandler I, Rangel-Escareño C, Orozco L, Aguilar-Delfín I, Vázquez-Pérez JA, Zúñiga J, Pérez-Patrigeon S, Espinosa E. A transcriptome-based model of central memory CD4 T cell death in HIV infection. BMC Genomics. 2016 Nov 22;17(1):956.

Saúl Lira-Albarrán, Marco F Larrea-Schiavon, Leticia González, Marta Durand, Claudia Rangel*, Fernando Larrea*. The effects of levonorgestrel on FSH-stimulated primary rat granulosa cell cultures through gene expression profiling are associated to hormone and folliculogenesis processes. Molecular and Cellular Endocrinology 2016 Sept. 20;       http://dx.doi.org/10.1016/j.mce.2016.09.020

Ortega-Gómez, Alette; Rangel-Escareño, Claudia*; Molina-Romero, Camilo; Macedo-Perez, Eleazar; Avilés, Alejandro; Lara-García, Alejandra; Rodríguez-Bautista, Rubén; Hidalgo-Miranda, Alfredo; Arrieta, Oscar*. Gene-expression profiles in lung adenocarcinomas related to chronic wood smoke or tobacco exposure. Respir Res. 2016 Apr 20;17:42. doi: 10.1186/s12931-016-0346-3.

Salido‑Guadarrama, A.I., Morales‑Montor, J.G., RangelEscareño, C., Langley, E., Peralta‑Zaragoza, O., Cruz Colin, J.L., & Rodriguez‑Dorantes, M. Urinary microRNA-based signature improves accuracy of detection of clinically relevant prostate cancer within the prostate-specific antigen grey zone. Mol Med Rep. 2016 Jun;13(6):4549-60. doi: 10.3892/mmr.2016.5095. Epub 2016 Apr 8.

Edith A. Fernández-Figueroa, Iván Imaz-Rosshandler, Juan E. Castillo-Fernández, Haydee Miranda-Ortíz, Juan C. Fernández-López, Ingeborg Becker2∗ and Claudia Rangel-Escareño*. Down-regulation of TLR and JAK/STAT pathway genes is associated with diffuse cutaneous leishmaniasis: a gene expression analysis in NK cells from patients infected with L. mexicana. PLoS Negl Trop Dis. 2016 Mar 31;10(3):e0004570. doi: 10.1371/journal.pntd.0004570.

Arturo Lopez Pineda, Henry Ato Ogoe, Jeya Balaji Balasubramanian, Claudia Rangel Escareño, Shyam Visweswaran, James Gordon Herman, Vanathi Gopalakrishnan. On Predicting Lung Cancer Subtypes using ‘Omic’ Data from Tumor and Tumor-Adjacent Histologically-Normal Tissue. BMC Cancer. (2016) Mar 4;16(1):184. doi: 10.1186/s12885-016-2223-3.

Checa M, Hagood JS, Velazquez-Cruz R, Ruiz V, García-De-Alba C, Rangel-Escareño C,     Francisco Urrea, Carina Becerril , Martha Montaño, Semiramis García-Trejo, José Cisneros Lira, Arnoldo Aquino-Gálvez, Annie Pardo, Moisés Selman. Cigarette Smoke Enhances the Expression of Profibrotic Molecules in Alveolar Epithelial Cells. PLoS One. 2016 Mar 2;11(3):e0150383. doi: 10.1371/journal.pone.0150383. eCollection 2016.

Bermúdez M, Imaz-Rosshandler I, Rangel-Escareño C, Zeichner-David M, Arzate H, Mercado-Celis GE CEMP1 Induces Transformation in Human Gingival Fibroblasts. PLoS ONE (2015), 10(5): e0127286. doi:10.1371/journal.pone.0127286

Contreras AV, Rangel-Escareño C, Torres N, Alemán-Escondrillas G, Ortiz V, Noriega LG, Torre-Villalvazo I, Granados O, Velázquez-Villegas LA, Tobon-Cornejo S, González-Hirschfeld D, Recillas-Targa F, Tejero-Barrera E, Gonzalez FJ, Tovar AR. PPARα via HNF4α regulates the expression of genes encoding hepatic amino acid catabolizing enzymes to maintain metabolic homeostasis. Genes Nutr. (2015) Mar;10(2):452. doi: 10.1007/s12263-014-0452-0. Epub 2015 Jan 10.

Vania Bonifaz-Peña, Alejandra V. Contreras, Claudio Jose Struchiner, Rosimeire A. Roela, Tatiane K. Furuya-Mazzotti, Roger Chammas, Claudia Rangel-Escareño, Laura Uribe-Figueroa, María José Gómez-Vázquez, Howard L. McLeod, Alfredo Hidalgo-Miranda, Esteban J. Parra, Juan Carlos Fernández-López, Guilherme Suarez-Kurtz. Exploring the Distribution of Genetic Markers of Pharmacogenomics Relevance in Brazilian and Mexican Populations. PLoS ONE November 24, 2014 DOI: 10.1371/journal.pone.0112640

Graciela Cárdenas, Gladis Fragoso, Marcos Rosetti, Laura Uribe‑Figueroa, Claudia RangelEscareño, Brenda Saenz, Marisela Hernández, Edda Sciutto and Agnes Fleury. Neurocysticercosis: the effectiveness of the cysticidal treatment could be influenced by the host immunity. Medical Microbiology and Immunology 203:373-381 December, 2014 doi:10.1007/s00430-014-0345-2

Sebastián Aguilar Pierlé*, Ivan Imaz Rosshandler, Ammielle Akim, Kerudin, Jacqueline Sambono, Ala Lew-Tabor, Peter Rolls, Claudia Rangel-Escareño, Kelly Brayton*. Genetic diversity of tick-borne rickettsial pathogens, insights gained from distant strains. Pathogens January (2014) 3, 57-72; doi:10.3390/pathogens3010057

Akinyemi I. Ojesina, Lee Lichtenstein, Samuel S. Freeman, Chandra Sekhar Pedamallu, Ivan Imaz-Rosshandler, Trevor J. Pugh, Andrew D. Cherniack, Lauren Ambrogio, Kristian Cibulskis, Bjørn Bertelsen, Sandra Romero-Cordoba, Victor Treviño, Karla Vazquez-Santillan, Alberto Salido Guadarrama, Alexi A.Wright, Mara W. Rosenberg, Fujiko Duke, Bethany Kaplan, Rui Wang, Elizabeth Nickerson, Heather M. Walline, Michael S. Lawrence, Chip Stewart, Scott L. Carter, Aaron McKenna, Iram P. Rodriguez-Sanchez, Magali Espinosa-Castilla, Kathrine Woie, Line Bjorge, Elisabeth Wik, Mari K. Halle, Erling A. Hoivik, Camilla Krakstad, Nayeli Belem Gabiño, Gabriela Sofia Gómez-Macías, Lezmes D. Valdez-Chapa, María Lourdes Garza-Rodríguez, German Maytorena, Jorge Vazquez, Carlos Rodea, Adrian Cravioto, Maria L. Cortes, Heidi Greulich, Christopher P. Crum, Donna S. Neuberg, Alfredo Hidalgo-Miranda, Claudia Rangel Escareno, Lars A. Akslen, Thomas E. Carey, Olav K. Vintermyr, Stacey B. Gabriel, Hugo A. Barrera-Saldaña, Jorge Melendez-Zajgla, Gad Getz, Helga B. Salvesen & Matthew Meyerson. Landscape of genomic alterations in cervical carcinomas. Nature (2014) February 20,2014

Héctor Rueda-Zarate, Ivan Imaz-Rosshandler, Julieta Noguez-Monroy and Claudia Rangel-Escareno. A gene expression landscape of drug-induced liver hepatotoxicity. Proceedings of the 13th International conference for the Critical Assessment of Massive Data Analysis CAMDA 2013.

Laura Adalid, Arce-Sillas Asiel, Gladis Fragoso, Cárdenas Graciela, Rosetti Marco, Casanova-Hernández Didier, Rangel-Ecareño Claudia, Uribe-Figueroa Laura, Agnes Fleury and Edda Sciutto. Cysticerci drive dendritic cells to promote in vitro and in vivo Tregs differentiation. Clinical and Developmental Immunology (2013) ISSN: 1740-2530 http://dx.doi.org/10.1155/2013/981468

Peñuelas Urquides, K., González Escalante, L., Villarreal Treviño L., Silva Ramírez B., Gutiérrez Fuentes, D.J.,Mojica Espinosa, R., Rangel Escareño, C., Uribe Figueroa, L., Molina Salinas, G.M., Dávila Velderrain, J.,Castorena Torres, F., Bermúdez de León, M., and Said Fernández, S. Comparison of gene expression profiles between pansensitive and multidrug-resistant strains of Mycobacterium tuberculosis. Current Microbiology (2013) Sep;67(3):362-71 doi 10.1007/s00284-013-0376-8

Mendoza C, Jiménez AV, Rangel C, Lozano A, Morales V, Becerril C, Chavira R, Ruiz V, Barrera L, Montaño M, Pardo A, Selman M. DHEA has strong antifibrotic effects and is decreased in idiopathic pulmonary fibrosis. Eur Respir J. (2013) 42:1309-1321. doi: 10.1183/09031936.00027412

Baca-Lopez K, Correa-Rodriguez MD, Flores-Espinosa R, Garcia-Herrera R, Hernandez-Armenta CI, Hidalgo-Miranda A, Huerta-Verde AJ, Imaz-Rosshandler I, Martinez-Rubio AV, Medina-Escareno A, Mendoza-Smith R, Rodriguez-Dorantes M, Salido-Guadarrama I, Hernandez-Lemus E and Rangel-Escareno C. A three-state model for multidimensional genomic data integration. Systems Biomedicine Volume 1, Issue 2,(2013) 2162-8130 (Print), 2162-8149 (Online)

Shantanu Banerji*, Kristian Cibulskis*, Claudia Rangel-Escareno*, Kristin K. Brown, Scott L. Carter, Abbie M. Frederick, Michael S. Lawrence, Andrey Y. Sivachenko, Carrie Sougnez, Lihua Zou, Maria L. Cortes, Juan C. Fernandez-Lopez, Shouyong Peng, Kristin G. Ardlie, Daniel Auclair, Veronica Bautista-Piña, Fujiko Duke, Joshua Francis, Antonio Maffuz-Aziz, Robert C. Onofrio, Melissa Parkin, Nam Pho, Valeria Quintanar-Jurado, Alex H. Ramos, Rosa Rebollar-Vega, Sergio Rodriguez-Cuevas, Sandra L. Romero-Cordoba, Steven E. Schumacher, Nicolas Stransky, Kristin M. Thompson, Laura Uribe-Figueroa, Jose Baselga, Rameen Beroukhim, Kornelia Polyak, Dennis C. Sgroi, Andrea L. Richardson, Gerardo Jimenez-Sanchez, Eric S. Lander, Stacey B. Gabriel, Levi A. Garraway, Todd R. Golub, Jorge Melendez-Zajgla, Alex Toker, Gad Getz, Alfredo Hidalgo-Miranda, and Matthew Meyerson. “Sequence analysis of mutations and translocation across breast cancer subtypes”. Nature (2012) (*) co-first author

Jens G. Lohr, Petar Stojanov, Michael S. Lawrence, Daniel Auclair, Bjoern Chapuy, Carrie Sougnez, Peter Cruz-Gordillo, Birgit Knoechel, Yan W Asmann, Susan L. Slager, Anne J. Novak, Ahmet Dogan,Stephen M Ansell, Brian K Link, Lihua Zou, Joshua Gould, Gordon Saksena, Nicolas Stransky, Claudia Rangel-Escareno, Juan Carlos Fernandez-Lopez, Alfredo Hidalgo-Miranda, Jorge Melendez-Zajgla, Enrique Hernandez-Lemus, Angela Schwarz-Cruz y Celis, Ivan Imaz-Rosshandler, Akinyemi Ojesina, Joonil Jung, Chandra Pedamallu, Eric S. Lander, Thomas M. Habermann, James R. Cerhan, Margaret Shipp, Gad Getz, Todd R Golub. Discovery and Prioritization of Somatic Mutations in DLBCL by Whole Exome Sequencing. PNAS (2012)

Edith A. Fernández-Figueroa, Claudia Rangel-Escareño, Valeria Espinosa-Mateos, Karol Carrillo-Sánchez, Norma Salaiza-Suazo, Georgina Carrada-Figueroa, Santiago March-Mifsut and Ingeborg Becker. Disease severity in patients infected with Leishmania mexicana relates to IL-1β. PLoS Neglected Tropical Diseases (2012) ISSN: 1935-2735

E.A. Fernández Figueroa, C. Rangel, V. Espinosa, K. Carrillo, N. Salaiza, I. Imaz and I. Becker. Looking for susceptibility factors in patients with cutaneous leishmaniasis from Tabasco, Mexico. Immunology (2011) Vol.35, Suppl.1, pp-145. Dec. 2011 ISSN:1365-2567

Jiménez-López S, Mancera-Martínez E, Donayre-Torres A, Rangel-Escareño C, Uribe Figueroa L, March-Mifsut S, Jiménez-Sánchez G and Sanchez de Jimenez E. Expression Profile of Maize Zea mays Embryonic Axes During Germination: Translational Regulation of Ribosomal Protein mRNAs. Plant and Cell Physiology (2011) Oct; 52(10):1719-33. Epub 2011 Aug 31

Nicolas Stransky, Ann Marie Egloff, Aaron D. Tward, Aleksandar D. Kostic, Kristian Cibulskis, Andrey Sivachenko, Gregory V. Kryukov, Michael S. Lawrence, Carrie Sougnez, Aaron McKenna, Erica Shefler Alex H. Ramos, Petar Stojanov, Scott L. Carter, Douglas Voet, Maria L Cortés, Daniel Auclair, Michael F. Berger, Gordon Saksena, Candace Guiducci, Robert Onofrio, Melissa Parkin, Marjorie Romkes, Joel L. Weissfeld, Raja R. Seethala, Lin Wang, Claudia Rangel-Escareño, Juan Carlos Fernandez-Lopez, Alfredo Hidalgo-Miranda, Jorge Melendez-Zajgla, Wendy Winckler, Kristin Ardlie, Stacey B. Gabriel, Matthew Meyerson, Eric S. Lander, Gad Getz, Todd R. Golub, Levi A. Garraway, Jennifer R. Grandis. The mutational landscape of head and neck squamous cell carcinoma. Science (2011) Aug 26;333(6046):1157-60. Epub 2011 Jul 28

Maria E Frigolet, Nimbe Torres, Laura Uribe-Figueroa, Claudia Rangel, Gerardo Jimenez-Sanchez and Armando R. Tovar. White adipose tissue genome wide-expression profiling and adipocyte metabolic functions after soy protein consumption in rats. Journal of Nutritional Biochemistry May 13 (2011)

Rangel-Escareño, I. Aguilar-Delfín and D. L. Wild. Inference of Key Transcriptional Regulators in Endothelial Cell Apoptosis using Bayesian State Space Models. Proceedings of the 8th International conference for the Critical Assessment of Microarray Data Analysis CAMDA pp:58-62 (2008)

D Mendoza-Villanueva, J Diaz-Chavez, L Uribe-Figueroa, C Rangel-Escareno, A Hidalgo-Miranda, S March-Mifsut, G Jimenez-Sanchez, P F Lambert and P Gariglio. Gene expression profile of cervical and skin tissues from human papillomavirus type 16 E6 transgenic mice. BMC Cancer (2008), 8:347

Louise Hull, Claudia Rangel Escareno, Jane M. Godsland, John R. Doig, Claire M. Johnson, Stephen C. Phillips, Stephen K. Smith, Simon Tavaré, Cristin G. Print, and D. Stephen Charnock-Jones. Endometrial-Peritoneal Interactions during Endometriotic Lesion Establishment. American J Pathology August 7, (2008). doi:10.2353/ajpath.2008.071128

Beal, M.J., Falciani, F., Ghahramani, Z., Rangel C. and Wild, D.L. “A Bayesian approach to reconstructing genetic regulatory networks with hidden factors.” Bioinformatics, 21: 349-356 (2005).

Rangel, C., Angus, J., Ghahramani, Z., Lioumi, M., Sotheran, E., A., Gaiba, A.,.Wild, D.L. and Falciani, F. “Modeling T-cell activation using gene expression profiling and state space models.” Bioinformatics (2004), 20(9):1361-1372.

Dubey, A., Hwang, S., Rangel, C., Rasmussen, C.E., Ghahramani, Z. and Wild, D.L. “Clustering protein sequence and structure space with infinite Gaussian mixture models.” Pacific Symposium in Biocomputing. Ed. R.B. Altman, A.K. Dunker, L. Hunter and T.E. Klein. World Scientific Publishing, Singapore, 399-410 (2004).

Rangel, C., Wild, D. L. Falciani, F., Ghahramani, Z., and Gaiba, A. “Modeling biological responses using gene expression profiling and linear dynamical systems.” Proceedings of the 2nd International Conference on Systems Biology. ISBN 1-59135-000-X Madison, WI: OmniPress, pp 248-256. (2001)

Book Chapters

  • “The role of information theory in gene regulatory network inference.” Hernandez-Lemus E., Rangel-Escareño C.  Information Theory: New Research, Nova Publishing (2012)
  • “Inferring Transcriptional Networks using Prior Biological Knowledge and Constrained State Space Models,”  John Angus, Matthew J. Beal, Juan Li, Claudia Rangel and David L. Wild, chapter in Learning and Inference in Computational Systems Biology, Neil D. Lawrence, Mark Girolami, Magnus Rattray, Guido Sanguinetti. The MIT Press Cambridge, Massachusetts London, England (2010)
  • “Modeling genetic regulatory networks using gene expression profiling and state space models,” C. Rangel,  J. Angus, Z. Ghahramani, and D. Wild, chapter in Applications of Probabilistic Modeling in Medical Informatics and Bioinformatics, D. Husmeier, S. Roberts, and R. Dybowski, editors, Springer Verlag, (2005).

Invited Talks

  • Warwick Sistems Biology Centre Seminar, University of Warwick July 11, 2011. “Comprehensive overview of intrinsic Breast cancer subtypes in Mexican and Vietnamese populations”
  • Week on Bioinformatics, Statistical Genetics, and Survival Analysis PASI: Panamerican Advanced Studies Institute, Centro de Investigación en Matemáticas CIMAT Mayo 2-5, 2010. Two talks: “Application of Di-base sequencing to SNPs detection in the AB SOLiDTM system”,  and “Learning and Inference in Computational Systems Biology”
  • 3er Jornada de Bioinformática Colegio de Posgraduados Campus Montecillo, Texcoco Edo. de México Septiembre 20-24, 2010. “Inferencia y aprendizaje en Biología se Sistemas”
  • Semana Nacional de Bioinformática NNB-2010, Centro de Ciencias Genómicas UNAM, Cuernavaca Morelos, México. Agosto 2-6, 2010. “Algoritmos de alineamiento global y local en secuenciación masiva”
  • Summer Workshop Instituto Tecnológico y de Estudios Superiores de Monterrey, Campus Cd. de México Julio 26-28, 2010 “Nuevas aplicaciones matemáticas y físicas: Genómica, Biología Molecular, Bioinformática y Medicina”
  • Semana de Bioinformática, Bioestadística y Análisis de Supervivencia dentro del Instituto Panamericano de Estudios Avanzados en Probabilidad y Estadística, PASI. CIMAT, Guanajuato, GTO. Mayo 1-8, 2010 “Inference and Learning in Computational Systems Biology”
  • Segunda Semana de Estadística en la Ciencia y la Tecnología, del 22 al 26 de Marzo del 2010; ITESM Campus Cd. México; “La estadística en el estudio del genoma humano”.
  • Instituto Panamericano De Estudios Avanzados En Probabilidad y Estadística , del 24 de Abril al 8 de Mayo 2010. Guanajuato, México. Organized by The National Science Foundation, Rice University and CIMAT. Semana de Bioinformática, Bioestadística, Análisis de Supervivencia.  “Learning and Inference in Computational Systems Biology”
  • Métodos Estadísticos y Analíticos de Datos Genómicos, Instituto de Biotecnología UNAM, Enero 18-22, 2010. “Análisis estadístico de datos con microarreglos de expresión usando R y Bioconductor”
  • Claremont Center for the Mathematical Sciences, Math-in-Industry workshop Claremont CA,  July 21-27, 2009. Presenting a problem with unknown answer to work with a group of students and 3 faculty members. Problem title: “A two-base encoded DNA sequence alignment problem in computational biology” http://ccms.claremont.edu/mini/problems/national-institute-genomic-medicine
  • Seminario de Matemáticas Aplicadas y Computación FES Acatlán, Naucalpan Edo. México; March 25, 2009. Implementación de un modelos de espacio-estado para inferir la dinámica de regulación de genes.
  • 1st Canada-Mexico Statistics Meeting February 22-23, 2008. Guanajuato, Gto., México Session on Genetics Statistics. “Dynamic Modeling of Gene Expression Data”
  • Matilde Representación de Matemáticas Aplicadas – XVI Semana de Matemáticas Aplicadas; Instituto Tecnológico Autónomo de México; Septiembre 2006. “Aplicaciones Matemáticas en la Medicina Genómica”
  • Seminar for Statistics – ETH Federal Institute of Technology; Zurich, Switzerland; April 21, 2005. “Applicability of Linear Dynamical Systems to Genetic Regulatory Network Inference”
  • Biomedical Engineering, USC Viterbi School of Engineering, February 28, 2005. “Using microarray gene expression data to infer genetic regulatory networks: a Linear Dynamical Systems Approach”
  • Complex Stochastic Systems in Biology and Medicine workshop; Munich, Germany  October 7-8, 2004. “Linear Dynamical Systems Modeling of Genetic Regulatory Networks.”
  • Retreat of the Joint Ph.D. Program in Computational Science Claremont Graduate University and San Diego State University, Temecula CA. November 2002. “Some Computational Aspects of Linear Dynamical Systems in their Use in Modeling Microarray Gene Expression Data,”
  • Gene Regulatory Network Workshop, Keck Graduate Institute, Claremont CA. June 2002. “Modeling Biological Responses using Gene Expression Profiling and Linear Dynamical Systems.”

 

Other Academic Activities

  • Claremont Colleges Math-in-Industry workshop; July 2009.
    “A two-base encoded DNA sequence alignment problem in computational biology”

 

Current Students

  • Iván Imaz-Rosshandler, Research Assistant August 2009 – Present
  • Rodrigo Mendoza-Smith,  Applied Mathematics ITAM
    Probei scholarship fellow September 2010 – August 2011
    Currently INMEGEN
    Project: Next generation sequencing algorithms
  • Claudia Hernandez-Armenta, Genomic Sciences UNAM
    Probei scholarship fellow February 2011 – August 2011
    Currently INMEGEN
    Project: Microarray data analysis of obesity in baboons

 

Former Students

  • Erika Lagos, Applied Mathematics ITAM
    Project: Monte Carlo feature selection for supervised classification of microarray gene expression data
    Currently MBA student Stanford University
  • Guilhem Richard, Visiting Scholar  INSA-Lyon, France February – June 2009
    Project: Mexican-Mestizo HapMap (Increasing SNP density by combining 3 platforms)
    Currently PhD student Bioinformatics at Boston University
  • Viviana García Horton, Applied Mathematics ITAM
    Probei scholarship fellow September 2008 – April 2009
    Project: R implementation of Affymetrix Exon arrays low-level analysis
    Currently PhD. student Statistics  at Harvard University
  • Valeria Espinosa Mateos, Applied Mathematics ITAM
    Research internship June 2007 – May 2008
    Project: R implementation and analysis of algorithms for Copy Number Variation analysis
    Currently PhD. student Statistics at Harvard University