Computational Genomics Program
Primera egresada de la Licenciatura en Ciencias Genómicas que recibe el grado de doctor
Compartimos el gusto y orgullo de la noticia de que Alejandra Medina se ha recibido hoy viernes 24 de febrero con el grado de Doctor en Ciencias Biomédicas en la UNAM. Se trata del primer egresado de la Licenciatura en Ciencias Genómicas que se recibe de doctorado.
Vacantes
Tenure track professor position and postdoctoral position to work in the computational genomics laboratory (http://www.ccg.unam.mx/en/ComputationalGenomics) at the Center for Genomic Sciences (CCG) within the National Autonomous University of Mexico (UNAM) in Cuernavaca, Morelos, Mexico. Our research focuses in regulation of gene expression in Escherichia coli and related bacteria.
Publicaciones
| # | Año | Ficha | Ligas |
| 1 | 2013 | Keseler, I.M., Mackie, A., Peralta-Gil, M., Santos-Zavaleta, A., Gama-Castro, S., Bonavides-Martínez, C., Fulcher, C., Huerta, A.M., Kothari, A., Krummenacker, M., Latendresse, M., Muñíz-Rascado, L., Ong, Q., Paley, S., Schroder, I., Shearer, A.G., Subhraveti, P., Travers, M., Weerasinghe, D., Weiss, V., Collado-Vides, J., Gunsalus, R.P., Paulsen, I. and Karp, P.D. (2013). "EcoCyc: Fusing Model Organism Databases With Systems Biology". Nucl Acid Res. 41(D1):D605-D612 | |
| 2 | 2013 | Salgado, H., Peralta-Gil, M., Gama-Castro, S., Santos-Zavaleta, A., Muñíz-Rascado, L., García-Sotelo, J., Weiss, V., Solano-Lira, H., Martínez-Flores, I., Medina-Rivera, A., Salgado-Osorio, G., Alquicira-Hernández, S., Alquicira-Hernández, K., López-Fuentes, A., Porrón-Sotelo, L., Huerta, A.M., Bonavides-Martínez, C., Balderas-Martinez, Y.I., Pannier, L., Olvera, M., Labastida, A., Jiménez-Jacinto, V., Vega-Alvarado, L., Del-Moral, V., Hernández-Álvarez, A., Morett, E. and Collado-Vides, J. (2013). "RegulonDB V8.0: Omics Data Sets, Evolutionary Conservation, Regulatory Phrases, Cross-validated Gold Standards And More". Nucl Acid Res. 41(D1):D203-D213 | PUBMED: #23203884 |
| 3 | 2012 | Pauling, J., Rottger, R., Neuner, A., Salgado, H., Collado-Vides, J., Kalaghatgi, P., Azevedo, V., Tauch, A., Puhlerg, A. and Baumbach, J. (2012). "On the Trail of EHEC/EAEC-unraveling the Gene Regulatory Networks of Human Pathogenic Escherichia coli Bacteria". Integr Biol-uk. 4(7):728-733 | PUBMED: #22318347 |
| 4 | 2012 | Salgado, H., Martínez-Flores, I., López-Fuentes, A., García-Sotelo, J., Porrón-Sotelo, L., Muñíz-Rascado, L. and Collado-Vides, J. (2012). "Extracting Regulatory Networks Of Escherichia coli From RegulonDB". Methods in Molecular Biology. 804:179-195 | PUBMED: #22144154 |
| 5 | 2011 | Álvarez-Vásquez, F., Riezman, H., Hannun, Y.A. and Voit, E.O. (2011). "Mathematical Modeling And Validation Of the Ergosterol Pathway in saccharomyces cerevisiae". Plos One. 6(12) | PUBMED: #22194828 |
| 6 | 2011 | Gama-Castro, S., Salgado, H., Peralta-Gil, M., Santos-Zavaleta, A., Muñíz-Rascado, L., Solano-Lira, H., Jimenez-Jacinto, V., Weiss, V., García-Sotelo, J., López-Fuentes, A., Porrón-Sotelo, L., Alquicira-Hernández, S., Medina-Rivera, A., Martínez-Flores, I., Alquicira-Hernández, K., Martínez-Adame, R., Bonavides-Martínez, C., Miranda-Ríos, J., Huerta, A.M., Mendoza-Vargas, A., Collado Torres, L., Taboada, B., Vega-Alvarado, L., Olvera, M., Olvera, L., Grande, R., Morett, E. and Collado-Vides, J. (2011). "RegulonDB Version 7.0: Transcriptional Regulation Of Escherichia coli K-12 Integrated within Genetic Sensory Response Units (gensor Units)". Nucl Acid Res. 39:D98-D105 | PUBMED: #21051347 |
| 7 | 2011 | Keseler, I.M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muñíz-Rascado, L., Bonavides-Martínez, C., Paley, S., Krummenacker, M., Altman, T., Spaulding, A., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A.G., Mackie, A., Paulsen, I., Gunsalus, R.P. and Karp, P.D. (2011). "EcoCyc: A Comprehensive Database Of Escherichia coli Biology". Nucl Acid Res. 39:D583-D590 | PUBMED: #21097882 |
| 8 | 2011 | Medina-Rivera, A., Abreu-Goodger, C., Thomas-Chollier, M., Salgado, H., Collado-Vides, J. and Van Helden, J. (2011). "Theoretical and Empirical Quality Assessment of Transcription Factor-binding Motifs". Nucl Acid Res. 39(3):808-824 | PUBMED: #20923783 |
| 9 | 2011 | Santos-Zavaleta, A., Gama-Castro, S. and Pérez-Rueda, E. (2011). "A Comparative Genome Analysis of the RpoS Sigmulon Shows a High Diversity of Responses and Origins". Microbiology-sgm. 157:1393-1401 | PUBMED: #21310789 |
| 10 | 2011 | Thomas-Chollier, M., Defrance, M.D.C., Medina-Rivera, A., Sand, O., Herrmann, C., Thieffry, D. and van Helden, J. (2011). "RSAT 2011: Regulatory Sequence Analysis Tools". Nucl Acid Res. 39 | PUBMED: #21715389 |
| 11 | 2010 | Demir, E., Cary, M.P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G.N., D Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martínez-Flores, I., Hu, Z.J., Jiménez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., López-Fuentes, A.C., Mi, H.Y., Pichler, E., Rodchenkov, I., Splendiani, A., Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, O., Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray-Rust, P., Neumann, E., Reubenacker, O., Samwald, M., van Iersel, M., Wimalaratne, S., Allen, K., Braun, B., Whirl-Carrillo, M., Cheung, K.H., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren L.Y., Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K.H., Rzhetsky, A., Schachter, V., Sobral, B., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado-Vides, J., Goto, S., Hucka, M., Le Novere, N., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P.D., Sander, C. and Bader, G.D. (2010). "The BioPAX Community Standard for Pathway Data Sharing". Nat Biotechnol. 28(9):935-942 | PUBMED: #20829833 |
| 12 | 2010 | Martínez-Flores, I., Jiménez-Jacinto, V., López-Fuentes, A. and Collado-Vides, J. (2010). "Expanding BioPAX Format By Integrating Gene Regulation". EMBnet.journal. 16:39-43 | |
| 13 | 2009 | Balleza, E., López-Bojorquez, L., Martínez-Antonio, A., Resendis-Antonio, O., Lozada-Chávez, I., Balderas-Martinez, Y.I., Encarnación, S. and Collado-Vides, J. (2009). "Regulation By Transcription Factors in Bacteria: beyond Description". FEMS Microbiol Rev. 33(1):133-151 | PUBMED: #19076632 |
| 14 | 2009 | Collado-Vides, J., Salgado, H., Morett, E., Gama-Castro, S., Jiménez-Jacinto, V., Martínez-Flores, I., Medina-Rivera, A., Muñíz-Rascado, L., Peralta-Gil, M. and Santos-Zavaleta, A. (2009). "Bioinformatics Resources for the Study of Gene Regulation in Bacteria". J Bacteriol. 191(1):23-31 | PUBMED: #18978060 |
| 15 | 2009 | González Pérez, A., Espinosa Angarica, V., Collado-Vides, J. and Vasconcelos, A.T. (2009). "From Sequence to Dynamics: the Effects of Transcription Factor and Polymerase Concentration Changes on Activated and Repressed Promoters". Bmc Mol Biol. 10(1):92 | PUBMED: #19772633 |
| 16 | 2009 | Janga, S.C., Salgado, H. and Martínez-Antonio, A. (2009). "Transcriptional Regulation Shapes the Organization of Genes on Bacterial Chromosomes". Nucl Acid Res. 37(11):3680-3688 | PUBMED: #19372274 |
| 17 | 2009 | Keseler, I.M., Bonavides-Martínez, C., Collado-Vides, J., Gama-Castro, S., Gunsalus, R.P., Johnson, D.A., Krummenacker, M., Nolan, L.M., Paley, S., Paulsen, I.T., Peralta-Gil, M., Santos-Zavaleta, A., Shearer, A.G. and Karp, P.D. (2009). "EcoCyc: A Comprehensive View Of Escherichia coli Biology". Nucl Acid Res. 37:D464-D470 | PUBMED: #18974181 |
| 18 | 2009 | Lemmens, K., De Bie, T., Dhollander, T., De Keersmaecker, S. C., Thijs, I. M., Schoofs, G., De Weerdt, A., De Moor, B., Vanderleyden, J., Collado-Vides, J., Engelen, K. and Marchal, K. (2009). "DISTILLER: A Data Integration Framework To Reveal Condition Dependency of Complex Regulons in Escherichia coli". Genome Biol. 10(3):R27 | PUBMED: #19265557 |
| 19 | 2009 | Lemmens, K., De Bie, T., Dhollander, T., Monsieurs, P., De Moor, B., Collado-Vides, J., Engelen, K. and Marchal, K. (2009). "The Condition-dependent Transcriptional Network in Escherichia coli". Ann. N. y. Acad. Sci.. 1158:29-35 | PUBMED: #19348629 |
| 20 | 2009 | Martínez-Antonio, A., Medina-Rivera, A. and Collado-Vides, J. (2009). "Structural and Functional Map of a Bacterial Nucleoid". Genome Biol. 10(12) | PUBMED: #19995411 |
| 21 | 2009 | Mendoza-Vargas, A., Olvera, L., Olvera, M., Grande, R., Vega-Alvarado, L., Taboada, B., Jiménez-Jacinto, V., Salgado, H., Juárez, K., Contreras-Moreira, B., Huerta, A.M., Collado-Vides, J. and Morett, E. (2009). "Genome-wide Identification Of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in e. coli.". Plos One. 4(10):e7526 | PUBMED: #19838305 |
| 22 | 2008 | Angarica, VE, Perez, AG, Vasconcelos, AT, Collado-Vides, J. and Contreras-Moreira, B. (2008). "Prediction of TF Target Sites Based on Atomistic Models of Protein-DNA Complexes". BMC Bioinformatics. 9:436 | PUBMED: #18922190 |
| 23 | 2008 | Freyre-González, J.A., Alonso-Pavón, J.A., Treviño, L.G. and Collado-Vides, J. (2008). "Functional Architecture Of Escherichia coli: New Insights Provided by a Natural Decomposition Approach". Genome Biol. 9(10):R154 | PUBMED: #18954463 |
| 24 | 2008 | Gama-Castro, S., Jiménez-Jacinto, V., Peralta-Gil, M., Santos-Zavaleta, A., Peñaloza-Spinola, M.I., Contreras-Moreira, B., Segura-Salazar, J., Muñíz-Rascado, L., Martínez-Flores, I., Salgado, H., Bonavides-Martínez, C., Abreu-Goodger, C., Rodríguez-Penagos, C., Miranda-Ríos, J., Morett, E., Merino, E., Huerta, A.M., Treviño, L.G. and Collado-Vides, J. (2008). "RegulonDB (version 6.0): Gene Regulation Model Of Escherichia coli K-12 beyond Transcription, Active (experimental) Annotated Promoters And Textpresso Navigation". Nucl Acid Res. 36:D120-D124 | PUBMED: #18158297 |
| 25 | 2008 | Hernández-Lucas, I., Gallego-Hernandez, A.L., Encarnación, S., Fernandez-Mora, M., Martínez-Batallar, Á.G., Salgado, H., Oropeza, R. and Calva, E. (2008). "The LysR-type Transcriptional Regulator Leuo Controls Expression of Several Genes in Salmonella enterica Serovar Typhi". J Bacteriol. 190(5):1658-1670 | PUBMED: #18156266 |
| 26 | 2008 | Hernandez-Romano, J, Carlos-Rivera, FJ, Salgado, H., Lamadrid-Figueroa, H, Valverde-Garduno, V, Rodriguez, MH and Martinez-Barnetche, J (2008). "Immunity Related Genes in Dipterans Share Common Enrichment of at-rich Motifs in their 5' Regulatory Regions that are Potentially Involved in Nucleosome Formation". BMC Genomics. 9:326 | PUBMED: #18613977 |
| 27 | 2008 | Janga, S.C., Collado-Vides, J. and Babu, M.M. (2008). "Transcriptional Regulation Constrains the Organization of Genes on Eukaryotic Chromosomes". P Nat Acad Sci USA. 105(41):15761-15766 | PUBMED: #18840678 |
| 28 | 2008 | Lozada-Chávez, I., Angarica, V.E., Collado-Vides, J. and Contreras-Moreira, B. (2008). "The Role of DNA-binding Specificity in the Evolution of Bacterial Regulatory Networks". J Mol Biol. 379(3):627-643 | PUBMED: #18466918 |
| 29 | 2008 | Perez, A.D.G., Gonzalez, E.G., Angarica, V.E., Vasconcelos, A.T.R. and Collado-Vides, J. (2008). "Impact of Transcription Units Rearrangement on the Evolution of the Regulatory Network of Gamma-proteobacteria". BMC Genomics. 9:128 | PUBMED: #18366643 |
| 30 | 2007 | Contreras-Moreira, B., Branger, P.A. and Collado-Vides, J. (2007). "TFmodeller: Comparative Modelling Of Protein-DNA Complexes". Bioinformatics. 23(13):1694-1696 | PUBMED: #17459960 |
| 31 | 2007 | Gehlenborg, N, Corpas, M and Janga, S.C. (2007). "Highlights from the Third International Society for Computational Biology Student Council Symposium at the Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology". BMC Bioinformatics. 8 | |
| 32 | 2007 | Gutierrez-Rios, R.M., Freyre-González, J.A., Resendis-Antonio, O., Collado-Vides, J., Saier, M. and Gosset, G. (2007). "Identification Of Regulatory Network Topological Units Coordinating the Genome-wide Transcriptional Response to Glucose in Escherichia coli". BMC Microbiol. 7 | PUBMED: #17559662 |
| 33 | 2007 | Janga, S.C. and Collado-Vides, J. (2007). "Structure and Evolution of Gene Regulatory Networks in Microbial Genomes". Res Microbiol. 158(10):787-794 | PUBMED: #17996425 |
| 34 | 2007 | Janga, S.C., Salgado, H., Collado-Vides, J. and Martínez-Antonio, A. (2007). "Internal versus External Effector And Transcription Factor Gene Pairs Differ in their Relative Chromosomal Position in Escherichia coli". J Mol Biol. 368(1):263-272 | PUBMED: #17321548 |
| 35 | 2007 | Janga, S.C., Salgado, H., Martínez-Antonio, A. and Collado-Vides, J. (2007). "Coordination Logic of the Sensing Machinery in the Transcriptional Regulatory Network of Escherichia coli". Nucl Acid Res. 35(20):6963-6972 | PUBMED: #17933780 |
| 36 | 2007 | Karp, P.D., Keseler, I.M., Shearer, A., Latendresse, M., Krummenacker, M., Paley, S.M., Paulsen, I., Collado-Vides, J., Gama-Castro, S., Peralta-Gil, M., Santos-Zavaleta, A., Peñaloza-Spinola, M.I., Bonavides-Martínez, C. and Ingraham, J. (2007). "Multidimensional Annotation Of the Escherichia coli K-12 Genome". Nucl Acid Res. 35(22):7577-7590 | PUBMED: #17940092 |
| 37 | 2007 | Palacios, R. and Collado-Vides, J. (2007). "Development of Genomic Sciences in Mexico: a Good Start and a Long Way to go". Plos Comput Biol. 3(9):1670-1673 | PUBMED: #17907791 |
| 38 | 2007 | Perez, A.G., Angarica, V.E., Vasconcelos, A.T.R. and Collado-Vides, J. (2007). "Tractor_DB (version 2.0): A Database of Regulatory Interactions in Gamma-proteobacterial Genomes". Nucl Acid Res. 35:D132-D136 | PUBMED: #17088283 |
| 39 | 2007 | Resendis-Antonio, O., Reed, J.L., Encarnación, S., Collado-Vides, J. and Palsson, B.O. (2007). "Metabolic Reconstruction And Modeling of Nitrogen Fixation in Rhizobium etli". Plos Comput Biol. 3(10):1887-1895 | PUBMED: #17922569 |
| 40 | 2007 | Rodríguez-Penagos, C., Salgado, H., Martínez-Flores, I. and Collado-Vides, J. (2007). "Automatic Reconstruction of a Bacterial Regulatory Network Using Natural Language Processing". BMC Bioinformatics. 8 | PUBMED: #17683642 |
| 41 | 2007 | Salgado, H., Martínez-Antonio, A. and Janga, S.C. (2007). "Conservation Of Transcriptional Sensing Systems in Prokaryotes: a Perspective from Escherichia coli". FEBS Lett. 581(18):3499-3506 | PUBMED: #17617412 |
| 42 | 2006 | Cabrera-Valladares, N., Richardson, A.P., Olvera, C., Treviño, L.G., Deziel, E., Lepine, F. and Soberón-Chávez, G. (2006). "Monorhamnolipids And 3-(3-hydroxyalkanoyloxy) Alkanoic Acids (HAAs) Production Using Escherichia coli as a Heterologous Host". Appl Microbiol Biotechnol. 73(1):187-194 | PUBMED: #16847602 |
| 43 | 2006 | Contreras-Moreira, B. and Collado-Vides, J. (2006). "Comparative Footprinting Of DNA-binding Proteins". Bioinformatics. 22(14):E74-E80 | PUBMED: #16873524 |
| 44 | 2006 | González, V., Santamaria, R.I., Bustos, P., Hernández-González, I., Medrano-Soto, A., Moreno-Hagelsieb, G., Janga, S.C., Ramírez-Romero, M.Á., Jiménez-Jacinto, V., Collado-Vides, J. and Dávila, G. (2006). "The Partitioned Rhizobium etli Genome: Genetic and Metabolic Redundancy in Seven Interacting Replicons". P Nat Acad Sci USA. 103(10):3834-3839 | PUBMED: #16505379 |
| 45 | 2006 | Huerta, A.M., Collado-Vides, J. and Francino, M.P. (2006). "Positional Conservation of Clusters of Overlapping Promoter-like Sequences in Enterobacterial Genomes". Mol Biol Evol. 23(5):997-1010 | PUBMED: #16547149 |
| 46 | 2006 | Huerta, A.M., Francino, M.P., Morett, E. and Collado-Vides, J. (2006). "Selection for Unequal Densities of Sigma(70) Promoter-like Signals in Different Regions of Large Bacterial Genomes". Plos Genet. 2(11):1740-1750 | PUBMED: #17096598 |
| 47 | 2006 | Janga, S.C., Lamboy, W.F., Huerta, A.M. and Moreno-Hagelsieb, G. (2006). "The Distinctive Signatures of Promoter Regions and Operon Junctions across Prokaryotes". Nucl Acid Res. 34(14):3980-3987 | PUBMED: #16914446 |
| 48 | 2006 | Lozada-Chávez, I., Janga, S.C. and Collado-Vides, J. (2006). "Bacterial Regulatory Networks are Extremely Flexible in Evolution". Nucl Acid Res. 34(12):3434-3445 | PUBMED: #16840530 |
| 49 | 2006 | Martínez-Antonio, A., Janga, S.C., Salgado, H. and Collado-Vides, J. (2006). "Internal-sensing Machinery Directs the Activity of the Regulatory Network in Escherichia coli". Trends Microbiol. 14(1):22-27 | PUBMED: #16311037 |
| 50 | 2006 | Moreno-Campuzano, S., Janga, S.C. and Perez-Rueda, E. (2006). "Identification and Analysis Of DNA-binding Transcription Factors in Bacillus Subtilis and other Firmicutes - a Genomic Approach". BMC Genomics. 7:147 | PUBMED: #16772031 |
| 51 | 2006 | Salgado, H., Gama-Castro, S., Peralta-Gil, M., Díaz-Peredo, E., Sánchez-Solano, F., Santos-Zavaleta, A., Martínez-Flores, I., Jiménez-Jacinto, V., Bonavides-Martínez, C., Segura-Salazar, J., Martínez-Antonio, A. and Collado-Vides, J. (2006). "RegulonDB (version 5.0): Escherichia coli K-12 Transcriptional Regulatory Network, Operon Organization, And Growth Conditions". Nucl Acid Res. 34:D394-D397 | PUBMED: #16381895 |
| 52 | 2006 | Salgado, H., Santos-Zavaleta, A., Gama-Castro, S., Peralta-Gil, M., Peñaloza-Spinola, M.I., Martínez-Antonio, A., Karp, P.D. and Collado-Vides, J. (2006). "The Comprehensive Updated Regulatory Network of Escherichia coli K-12". BMC Bioinformatics. 7:5 | PUBMED: #16398937 |
| 53 | 2005 | Espinosa, V., Gonzalez, A.D., Vasconcelos, A.T., Huerta, A.M. and Collado-Vides, J. (2005). "Comparative Studies of Transcriptional Regulation, Mechanisms in a Group of Eight Gamma-proteobacterial Genomes". J Mol Biol. 354(1):184-199 | PUBMED: #16236313 |
| 54 | 2005 | Flores, M., Morales, L., Ávila, A., González, V., Bustos, P., García-Alonso, D., Mora, Y., Guo, X.W., Collado-Vides, J., Pinero, D., Dávila, G., Mora, J. and Palacios, R. (2005). "Diversification of DNA Sequences in the Symbiotic Genome of Rhizobium etli". J Bacteriol. 187(21):7185-7192 | PUBMED: #16237002 |
| 55 | 2005 | Gonzalez, A.D., Espinosa, V., Vasconcelos, A.T., Perez-Rueda, E. and Collado-Vides, J. (2005). "Tractor_DB: A Database of Regulatory Networks in Gamma-proteobacterial Genomes". Nucl Acid Res. 33:D98-D102 | PUBMED: #15608293 |
| 56 | 2005 | Guerrero, G., Peralta, H., Aguilar, A., Díaz-Mendez, R., Villalobos-López, M.A., Medrano-Soto, A. and Mora, J. (2005). "Evolutionary, Structural And Functional Relationships Revealed by Comparative Analysis of Syntenic Genes in Rhizobiales". BMC Evol Biol. 5:55 | PUBMED: #16229745 |
| 57 | 2005 | Guia, M.H., Perez, A.G., Angarica, V.E., Vasconcelos, A.T. and Collado-Vides, J. (2005). "Complementing Computationally Predicted Regulatory Sites In Tractor_DB Using a Pattern Matching Approach". In Silico Biology. 5(2):209-219 | PUBMED: #15972018 |
| 58 | 2005 | Ibarra-Junquera, V., Torres, L.A., Rosu, H.C., Arguello, G. and Collado-Vides, J. (2005). "Nonlinear Software Sensor for Monitoring Genetic Regulation Processes with Noise and Modeling Errors". Phys Rev e. 72(1):11919 | PUBMED: #16090013 |
| 59 | 2005 | Janga, S.C., Collado-Vides, J. and Moreno-Hagelsieb, G. (2005). "Nebulon: a System for the Inference of Functional Relationships of Gene Products from the Rearrangement of Predicted Operons". Nucl Acid Res. 33(8):2521-2530 | PUBMED: #15867197 |
| 60 | 2005 | Keseler, I.M., Collado-Vides, J., Gama-Castro, S., Ingraham, J., Paley, S., Paulsen, I.T., Peralta-Gil, M. and Karp, P.D. (2005). "EcoCyc: A Comprehensive Database Resource For Escherichia coli". Nucl Acid Res. 33:D334-D337 | PUBMED: #15608210 |
| 61 | 2005 | Le Novere, N., Finney, A., Hucka, M., Bhalla, U.S., Campagne, F., Collado-Vides, J., Crampin, E.J., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, J.L., Spence, H.D. and Wanner, B.L. (2005). "Minimum Information Requested In the Annotation of Biochemical Models (MIRIAM)". Nat Biotechnol. 23(12):1509-1515 | PUBMED: #16333295 |
| 62 | 2005 | Medrano-Soto, A., Christen, J.A. and Collado-Vides, J. (2005). "Bclass: a Bayesian Approach Based on Mixture Models for Clustering and Classification of Heterogeneous Biological Data". J Stat Softw. 13(2):1-18 | |
| 63 | 2005 | Menchaca-Mendez, R., Janga, S.C. and Collado-Vides, J. (2005). "The Network of Transcriptional Interactions Imposes Linear Constrains in the Genome". Omics. 9(2):139-145 | PUBMED: #15969646 |
| 64 | 2005 | Ramirez, M., Graham, M.A., Blanco, L., Silvente, S., Medrano-Soto, A., Blair, M.W., Hernández, G., Vance, C.P. and Lara-Flores, M. (2005). "Sequencing and Analysis of Common Bean ESTs. Building a Foundation for Functional Genomics". Plant Physiol. 137(4):1211-1227 | PUBMED: #15824284 |
| 65 | 2005 | Resendis-Antonio, O., Freyre-González, J.A., Menchaca-Mendez, R., Gutiérrez-Ríos, R.M., Martínez-Antonio, A., Ávila-Sánchez, C. and Collado-Vides, J. (2005). "Modular Analysis of the Transcriptional Regulatory Network of e-coli". Trends Genet. 21(1):16-20 | PUBMED: #15680508 |
| 66 | 2004 | Janga, S.C. and Moreno-Hagelsieb, G. (2004). "Conservation of Adjacency as Evidence of Paralogous Operons". Nucl Acid Res. 32(18):5392-5397 | PUBMED: #15477389 |
| 67 | 2004 | Karp, P.D., Arnaud, M., Collado-Vides, J., Ingraham, J., Paulsen, I.T. and Saier, M.H. (2004). "The E-coli EcoCyc Database: no Longer Just a Metabolic Pathway Database". ASM News. 70(1):25-30 | |
| 68 | 2004 | Lamboy, W.F. and Moreno-Hagelsieb, G. (2004). "A New Method of Solution for the Occupancy Problem and Its Application to Operon Size Prediction". J Theor Biol. 227(3):315-322 | PUBMED: #15019498 |
| 69 | 2004 | Medrano-Soto, A., Moreno-Hagelsieb, G., Vinuesa, P., Christen, J.A. and Collado-Vides, J. (2004). "Successful Lateral Transfer Requires Codon Usage Compatibility between Foreign Genes And Recipient Genomes". Mol Biol Evol. 21(10):1884-1894 | PUBMED: #15240837 |
| 70 | 2004 | Oviedo, N.A., Salgado, H., Collado-Vides, J. and Guarneros, G. (2004). "Distribution of Minigenes in the Bacteriophage Lambda Chromosome". Gene. 329:115-124 | PUBMED: #15033534 |
| 71 | 2004 | Perez-Rueda, E., Collado-Vides, J. and Segovia, L. (2004). "Phylogenetic Distribution Of DNA-binding Transcription Factors in Bacteria and Archaea". Comput Biol Chem. 28(5-6):341-350 | PUBMED: #15556475 |
| 72 | 2004 | Resendis-Antonio, O. and Collado-Vides, J. (2004). "The Growth of Random Networks as a Diffusion Process". Physica a. 342(3-4):551-560 | |
| 73 | 2004 | Salgado, H., Gama-Castro, S., Martínez-Antonio, A., Díaz-Peredo, E., Sánchez-Solano, F., Peralta-Gil, M., García-Alonso, D., Jiménez-Jacinto, V., Santos-Zavaleta, A., Bonavides-Martínez, C. and Collado-Vides, J. (2004). "RegulonDB (version 4.0): Transcriptional Regulation, Operon Organization And Growth Conditions In Escherichia coli K-12". Nucl Acid Res. 32:D303-D306 | PUBMED: #14681419 |
| 74 | 2003 | Collado-Vides, J., Medrano-Soto, A. and Tusié-Luna, M.T. (2003). "With the Finished Human Genome in Hand, What next?". Genome Biol. 4(7):328 | PUBMED: #12844356 |
| 75 | 2003 | González, V., Bustos, P., Ramírez-Romero, M.Á., Medrano-Soto, A., Salgado, H., Hernández-González, I., Hernandez-Celis, J.C., Quintero, V., Moreno-Hagelsieb, G., Girard, L., Rodríguez, O., Flores, M., Cevallos, M.A., Collado-Vides, J., Romero, D. and Dávila, G. (2003). "The Mosaic Structure of the Symbiotic Plasmid of Rhizobium etli CFN42 and Its Relation to other Symbiotic Genome Compartments". Genome Biol. 4(6) | PUBMED: #12801410 |
| 76 | 2003 | Gutiérrez-Ríos, R.M., Rosenblueth, D.A., Loza, J.A., Huerta, A.M., Glasner, J.D., Blattner, F.R. and Collado-Vides, J. (2003). "Regulatory Network Of Escherichia coli: Consistency between Literature Knowledge And Microarray Profiles". Genome Res. 13(11):2435-2443 | PUBMED: #14597655 |
| 77 | 2003 | Huerta, A.M. and Collado-Vides, J. (2003). "Sigma70 Promoters In Escherichia coli: Specific Transcription In Dense Regions of Overlapping Promoter-like Signals". J Mol Biol. 333(2):261-278 | PUBMED: #14529615 |
| 78 | 2003 | Jauregui, R., Abreu-Goodger, C., Moreno-Hagelsieb, G., Collado-Vides, J. and Merino, E. (2003). "Conservation of DNA Curvature Signals in Regulatory Regions of Prokaryotic Genes". Nucl Acid Res. 31(23):6770-6777 | PUBMED: #14627810 |
| 79 | 2003 | Martínez-Antonio, A. and Collado-Vides, J. (2003). "Identifying Global Regulators in Transcriptional Regulatory Networks in Bacteria". Curr Opin Microbiol. 6(5):482-489 | PUBMED: #14572541 |
| 80 | 2003 | Martínez-Antonio, A., Salgado, H., Gama-Castro, S., Gutiérrez-Ríos, R.M., Jiménez-Jacinto, V. and Collado-Vides, J. (2003). "Environmental Conditions And Transcriptional Regulation in Escherichia coli: a Physiological Integrative Approach". Biotechnol Bioeng. 84(7):743-749 | PUBMED: #14708114 |
| 81 | 2003 | Perret, X., Kobayashi, H. and Collado-Vides, J. (2003). "Regulation Of Expression Of Symbiotic Genes in Rhizobium sp. NGR234". Indian Journal of Experimental Biology. 41(10):1101-1113 | PUBMED: #15242276 |
| 82 | 2003 | Valderrama, B., Oliver, P., Medrano-Soto, A. and Vazquez-Duhalt, R. (2003). "Evolutionary and Structural Diversity of Fungal Laccases". Anton Leeuwenhoek Int J Gen M. 84(4):289-299 | PUBMED: #14574106 |
| 83 | 2002 | Benítez-Bellón, E., Moreno-Hagelsieb, G. and Collado-Vides, J. (2002). "Evaluation of Thresholds for the Detection of Binding Sites for Regulatory Proteins in Escherichia coli K12 DNA.". Genome Biol. 3(3) | PUBMED: #11897025 |
| 84 | 2002 | Collado-Vides, J., Moreno-Hagelsieb, G. and Medrano-Soto, A. (2002). "Microbial Computational Genomics of Gene Regulation". Pure Appl Chem. 74(6):899-905 | |
| 85 | 2002 | de Daruvar, A., Collado-Vides, J. and Valencia, A. (2002). "Analysis of The Cellular Functions of Escherichia coli Operons and their Conservation in Bacillus Subtilis". J Mol Evol. 55(2):211-221 | PUBMED: #12107597 |
| 86 | 2002 | Degrave, W.M., Vargas, R., Alvarez, F., Collado-Vides, J., Nunez, L., Ramirez, J.L. and Grau, O. (2002). "Towards A Bioinformatics Network For Latin America and the Caribbean (LACBioNet).". Applied Bioinformatics. 1(1):53-56 | PUBMED: #15130857 |
| 87 | 2002 | Huerta, A.M., Glasner, J.D., Gutiérrez-Ríos, R.M., Blattner, F.R. and Collado-Vides, J. (2002). "GETools: Gene Expression Tool For Analysis Of Transcriptome Experiments in e. coli". Trends Genet. 18(4):217-218 | |
| 88 | 2002 | Karp, P.D., Riley, M., Saier, M., Paulsen, I.T., Collado-Vides, J., Paley, S.M., Pellegrini-Toole, A., Bonavides-Martínez, C. and Gama-Castro, S. (2002). "The EcoCyc Database". Nucl Acid Res. 30(1):56-58 | PUBMED: #11752253 |
| 89 | 2002 | Moreno-Hagelsieb, G. and Collado-Vides, J. (2002). "A Powerful Non-homology Method for the Prediction of Operons in Prokaryotes.". Bioinformatics. 18:S329-336 | PUBMED: #12169563 |
| 90 | 2002 | Moreno-Hagelsieb, G. and Collado-Vides, J. (2002). "Operon Conservation from the Point of View of Escherichia coli, and Inference of Functional Inter-dependence of Gene Products from Genome Context". In Silico Biology. 2(2):87-95 | PUBMED: #12066843 |
| 91 | 2001 | Hershberg, R., Bejerano, G., Santos-Zavaleta, A. and Margalit, H. (2001). "PromEC: An Updated Database Of Escherichia coli mRNA Promoters with Experimentally Identified Transcriptional Start Sites". Nucl Acid Res. 29(1):277-277 | PUBMED: #11125111 |
| 92 | 2001 | Moreno-Hagelsieb, G., Trevino, V., Pérez-Rueda, E., Smith, T.F. and Collado-Vides, J. (2001). "Transcription Unit Conservation In the Three Domains of Life: a Perspective from Escherichia coli". Trends Genet. 17(4):175-177 | PUBMED: #11275307 |
| 93 | 2001 | Pérez-Rueda, E. and Collado-Vides, J. (2001). "Common History at the Origin of the Position-function Correlation in Transcriptional Regulators in Archaea and Bacteria". J Mol Evol. 53(3):172-179 | PUBMED: #11523004 |
| 94 | 2001 | Ramírez-Benítez, M.D., Moreno-Hagelsieb, G. and Almagro, J.C. (2001). "VIR.II: a New Interface with the Antibody Sequences in the Kabat Database". Biosystems. 61(2-3):125-131 | PUBMED: #11716972 |
| 95 | 2001 | Ramírez-Santos, J., Collado-Vides, J., García-Varela, M. and Gómez-Eichelmann, M.C. (2001). "Conserved Regulatory Elements of the Promoter Sequence of the Gene RpoH of Enteric Bacteria". Nucl Acid Res. 29(2):380-386 | PUBMED: #11139607 |
| 96 | 2001 | Salgado, H., Santos-Zavaleta, A., Gama-Castro, S., Millán-Zárate, D., Díaz-Peredo, E., Sánchez-Solano, F., Pérez-Rueda, E., Bonavides-Martínez, C. and Collado-Vides, J. (2001). "RegulonDB (version 3.2): Transcriptional Regulation And Operon Organization In Escherichia coli K-12". Nucl Acid Res. 29(1):72-74 | PUBMED: #11125053 |
| 97 | 2001 | Tan, K., Moreno-Hagelsieb, G., Collado-Vides, J. and Stormo, G.D. (2001). "A Comparative Genomics Approach to Prediction of New Members of Regulons". Genome Res. 11(4):566-584 | PUBMED: #11282972 |
| 98 | 2000 | Pérez-Rueda, E. and Collado-Vides, J. (2000). "The Repertoire Of DNA-binding Transcriptional Regulators in Escherichia coli K-12". Nucl Acid Res. 28(8):1838-1847 | PUBMED: #10734204 |
| 99 | 2000 | Salgado, H., Moreno-Hagelsieb, G., Smith, T.F. and Collado-Vides, J. (2000). "Operons In Escherichia coli: Genomic Analyses and Predictions". P Nat Acad Sci USA. 97(12):6652-6657 | PUBMED: #10823905 |
| 100 | 2000 | Salgado, H., Santos-Zavaleta, A., Gama-Castro, S., Millán-Zárate, D., Blattner, F.R. and Collado-Vides, J. (2000). "RegulonDB (version 3.0): Transcriptional Regulation And Operon Organization In Escherichia coli K-12". Nucl Acid Res. 28(1):65-67 | PUBMED: #10592182 |
| 101 | 2000 | Strainic, M.G., Sullivan, J.J., Collado-Vides, J. and deHaseth, P.L. (2000). "Promoter Interference in a Bacteriophage Lambda Control Region: Effects of a Range of Interpromoter Distances". J Bacteriol. 182(1):216-220 | PUBMED: #10613884 |
| 102 | 2000 | van Helden, J., Andre, B. and Collado-Vides, J. (2000). "A Web Site for the Computational Analysis of Yeast Regulatory Sequences". Yeast. 16(2):177-187 | PUBMED: #10641039 |
| 103 | 2000 | van Helden, J., Ríos, A.F. and Collado-Vides, J. (2000). "Discovering Regulatory Elements in Non-coding Sequences by Analysis of Spaced Dyads". Nucl Acid Res. 28(8):1808-1818 | PUBMED: #10734201 |
| 104 | 1999 | Collado-Vides, J., Hofestadt, R., Mavrovouniotis, M. and Michal, G. (1999). "Modeling and Simulation of Gene Regulation and Metabolic Pathways". Biosystems. 49(1):79-82 | PUBMED: #10091975 |
| 105 | 1999 | Salgado, H., Santos-Zavaleta, A., Garza-Ramos, U., van Helden, J., Díaz-Peredo, E. and Collado-Vides, J. (1999). "RegulonDB (version 2.0): A Database On Transcriptional Regulation in Escherichia coli". Nucl Acid Res. 27(1):59-60 | PUBMED: #9847141 |
| 106 | 1998 | Collado-Vides, J., Gutiérrez-Ríos, R.M. and Bel-Enguix, G. (1998). "Networks of Transcriptional Regulation Encoded in a Grammatical Model". Biosystems. 47(1-2):103-118 | PUBMED: #9715754 |
| 107 | 1998 | Huerta, A.M., Salgado, H., Thieffry, D. and Collado-Vides, J. (1998). "RegulonDB: A Database On Transcriptional Regulation in Escherichia coli". Nucl Acid Res. 26(1):55-59 | PUBMED: #9399800 |
| 108 | 1998 | Pérez-Rueda, E., Gralla, J.D. and Collado-Vides, J. (1998). "Genomic Position Analyses and the Transcription Machinery". J Mol Biol. 275(2):165-170 | PUBMED: #9466899 |
| 109 | 1998 | Thieffry, D., Huerta, A.M., Pérez-Rueda, E. and Collado-Vides, J. (1998). "From Specific Gene Regulation To Genomic Networks: a Global Analysis of Transcriptional Regulation in Escherichia coli". Bioessays. 20(5):433-440 | PUBMED: #9670816 |
| 110 | 1998 | Thieffry, D., Salgado, H., Huerta, A.M. and Collado-Vides, J. (1998). "Prediction of Transcriptional Regulatory Sites in the Complete Genome Sequence of Escherichia coli K-12". Bioinformatics. 14(5):391-400 | PUBMED: #9682052 |
| 111 | 1998 | van Helden, J., Andre, B. and Collado-Vides, J. (1998). "Extracting Regulatory Sites from the Upstream Region of Yeast Genes by Computational Analysis of Oligonucleotide Frequencies". J Mol Biol. 281(5):827-842 | PUBMED: #9719638 |
| 112 | 1997 | Blattner, F.R., Plunkett, G., Bloch, C.A., Perna, N.T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F., Gregor, J., Davis, N.W., Kirkpatrick, H.A., Goeden, M.A., Rose, D.J., Mau, B. and Shao, Y. (1997). "The Complete Genome Sequence of Escherichia coli K-12". Science. 277(5331):1453-1462 | PUBMED: #9278503 |
| 113 | 1997 | Collado-Vides, J., Huerta, A.M. and Klose, K. (1997). "Three Models Of Gene Regulation in e-coli". Bioinformatics. 1278:72-78 | |
| 114 | 1997 | Thieffry, D. (1997). "Contributions of the \"rouge-cloitre Groupto\" the Notion of \"messenger RNA". Hist Phil Life Sci. 19(1):89-111 | PUBMED: #9284644 |
| 115 | 1997 | Thieffry, D., Rosenblueth, D.A., Huerta, A.M., Salgado, H. and Collado-Vides, J. (1997). "Definite-clause Grammars For the Analysis of CIS-regulatory Regions in e. coli". Pacific Symposium on Biocomputing. 441-452 | PUBMED: #9390313 |
| 116 | 1996 | Collado-Vides, J. (1996). "Towards A Unified Grammatical Model of Sigma 70 and Sigma 54 Bacterial Promoters". Biochimie. 78(5):351-363 | PUBMED: #8905154 |
| 117 | 1996 | Hofestadt, R., Mavrovouniotis, M., Collado-Vides, J. and Loffler, M. (1996). "Modeling and Simulation of Metabolic Pathways, Gene Regulation and Cell Differentiation - October 22-27, 1995. International Conference and Research Center for Computer Science, Schloss Dagstuhl, Saarland, Germany". Bioessays. 18(4):333-335 | PUBMED: #8967902 |
| 118 | 1996 | Rosenblueth, D.A., Thieffry, D., Huerta, A.M., Salgado, H. and Collado-Vides, J. (1996). "Syntactic Recognition Of Regulatory Regions in Escherichia coli". Comput Appl Biosci. 12(5):415-422 | PUBMED: #8996790 |
| 119 | 1996 | Thieffry, D. (1996). "Escherichia coli As a Model System with Which to Study Cell Differentiation". Hist Phil Life Sci. 18(2):163-193 | PUBMED: #9122371 |
| 120 | 1996 | Thieffry, D. and Burian, R.M. (1996). "Jean Brachet's Alternative Scheme for Protein Synthesis". Trends Biochem Sci. 21(3):114-117 | PUBMED: #8882586 |
| 121 | 1993 | Collado-Vides, J. (1993). "A Linguistic Representation of the Regulation of Transcription Initiation .1. an Ordered Array of Complex Symbols with Distinctive Features". Biosystems. 29(2-3):87-104 | PUBMED: #8374070 |
| 122 | 1993 | Collado-Vides, J. (1993). "A Linguistic Representation of the Regulation of Transcription Initiation .2. Distinctive Features of Sigma 70 Promoters and their Regulatory Binding-sites". Biosystems. 29(2-3):105-128 | PUBMED: #8374063 |
| 123 | 1993 | Collado-Vides, J. (1993). "The Elements for a Classification of Units of Genetic Information with a Combinatorial Component". J Theor Biol. 163(4):527-548 | PUBMED: #8246512 |
Trabajos y proyectos posdoctorales
Proyectos de Genomica Computacional
Programa de Genómica Computacional
Responsable: Julio Collado-Vides, Ph.D.
Con base en la anotación continua de la red de regulación más completa existente para una célula viva, Escherichia coli K-12 (modelada en las bases de datos RegulonDB y EcoCyc), nuestra investigación se relaciona con el diseño computacional, la predicción genómica y los análisis comparativo y evolutivo de la regulación de la expresión genética en bacterias.
Desarrollamos métodos de predicción de redes de regulación, factores de transcripción, promotores, operones y asociaciones funcionales entre los genes. Hemos iniciado modelos discretos de la red, comparada con datos de microarreglos; redefinido reguladores globales; analizado la topología de la red; y contribuido con nuevos análisis integrativos de regulación y censado. Además, estamos iniciando una etapa de verificación experimental del comportamiento predicho de la red.
Este programa ha proporcionado la bioinformática para la genómica en este Centro, en términos de investigación (anotación de bases de datos y análisis comparativos de la secuencia genómica de Rhizobium.etli), así como de educación. Diversos miembros del laboratorio están a cargo de cursos en ciencias computacionales, bioinformática y biología de sistemas en nuestros programas de Licenciatura en Ciencias Genómicas. Este programa tiene a su cargo las tecnologías de la información en el centro, así como el Nodo Nacional de Bioinformática UNAM (NNB-UNAM), el cual es miembro de la Red Europea de Biología Molecular (EMBnet).
La investigación que se realiza en el laboratorio está apoyada por fondos de la UNAM, el Conacyt, y los Institutos Nacionales de Salud (NIH) de los EU.
Genómica funcional en E. coli: Caracterización experimental y modelación de la red de regulación transcripcional
Posdoctoral fellow: Dr. Luis Gerardo Treviño Quintanilla.
Bioinformatic Systems Standardization
Posdoctoral fellow: Dr. Juan Segura Salazar.
Mining the text biobibliome for experimental evidence of predicted gene regulation in E. coli
Posdoctoral fellow: Carlos Rodríguez Penagos, Ph.D.
Identification of transcription factors binding motif in eukaryotic genomes
Lucia Nikolaia López Bojorquez, Ph.D.
Simulating regulatory networks in Escherichia coli by comparative modelling of transcription factors Posdoctoral fellow:
Dr. Bruno Contreras Moreira.
This project is about integrating experimental data related with gene
expression and genomic data through theoretical models in Escherichia
coli, using microarray data, RegulonDB and the Protein Data Bank (PDB).
RegulonDB
Curation and Computational Design of the Escherichia coli K-12 Transcriptional Regulatory Network, its Operon Organization, and Growth Conditions
RegulonDB (beta version) can be accessed at http://regulondb.ccg.unam.mx
Computational Predictions of Regulatory Genomic Elements Conforming Regulatory Networks
Context and History
Comparative and evolutionary analyses of gene regulation
Context and History
Ernesto Pérez-Rueda brought evolutionary analyses of gene regulation to this lab, when he expanded the repertoire of transcription factors of E.coli (Pérez-Rueda and Collado-Vides, 2000) to all the bacterial and archeal
genomes (Pérez-Rueda and Collado-Vides, 2001), showing that in fact some ancient families are shared between bacteria and archea.
GrEMBOSS Project
Responsable(s):
César Bonavides
Grupo de trabajo:
César Bonavides, CCG
Romualdo Zayas, CCG
Alfredo Hernández, CCG
Jerome Verleyen, IBt
Roberto Rodríguez, IBt
Eduardo Murrieta, DGSCA
Objetivo:
Run EMBOSS programs on the EELA Grid
Mail contacto:
gremboss-dev@ccg.unam.mx