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 2014 Frausto-Solis, J., Linan-García, E., Sánchez-Pérez, M. and Sánchez-Hernández, J.P. (2014). "Chaotic Multiquenching Annealing Applied to the Protein Folding Problem". Sci. World J..   PUBMED: #24790563
2 2014 Martinez, L.C., Martínez-Flores, I., Salgado, H., Fernández-Mora, M., Medina-Rivera, A., Puente, J.L., Collado-Vides, J. and Bustamante, V.H. (2014). "In Silico Identification and Experimental Characterization of Regulatory Elements Controlling the Expression of the Salmonella csrB and csrC Genes". J Bacteriol. 196(2):325-336   PUBMED: #24187088
3 2014 Meysman, P., Collado-Vides, J., Morett, E., Viola, R., Engelen, K. and Laukens, K. (2014). "Structural Properties of Prokaryotic Promoter Regions Correlate with Functional Features". Plos One. 9(2):e88717   PUBMED: #24516674
4 2014 Meysman, P., Sonego, P., Bianco, L., Fu, Q., Ledezma-Tejeida, D., Gama-Castro, S., Liebens, V., Laukens, K., Marchal, K., Collado-Vides, J. and Engelen, K. (2014). "Colombos V2.0: an ever Expanding Collection of Bacterial Expression Compendia". Nucl Acid Res. 42(D1):D649-D653   PUBMED: #24214998
5 2013 Balderas-Martinez, Y.I., Savageau, M., Salgado, H., Pérez-Rueda, E, Morett, E. and Collado-Vides, J. (2013). "Transcription Factors In Escherichia coli Prefer the Holo Conformation". Plos One. 8(6)   PUBMED: #23776535
6 2013 Frausto-Solis, J., Sánchez-Pérez, M., Linan-García, E., Sánchez-Hernández, J.P. and Ramachandran, M. (2013). "Cluster Perturbation Simulated Annealing for Protein Folding Problem". J. Univers. Comput. Sci.. 19(15):2207-2223    
7 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   PUBMED: #23143106
8 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
9 2013 Treviño, L.G., Freyre-González, J.A. and Martínez-Flores, I. (2013). "Anti-sigma Factors In e-coli: Common Regulatory Mechanisms Controlling Sigma Factors Availability". Curr. Genomics. 14(6):378-387   PUBMED: #24396271
10 2013 Weiss, V., Medina-Rivera, A., Huerta, A.M., Santos-Zavaleta, A., Salgado, H., Morett, E. and Collado-Vides, J. (2013). "Evidence Classification Of High-throughput Protocols and Confidence Integration in RegulonDB". Database-the Journal of Biological Databases and Curation.   PUBMED: #23327937
11 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
12 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
13 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
14 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
15 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
16 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
17 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
18 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
19 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
20 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    
21 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
22 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
23 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
24 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
25 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
26 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
27 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
28 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
29 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
30 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
31 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
32 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
33 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
34 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
35 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
36 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
37 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
38 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
39 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    
40 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
41 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
42 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
43 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
44 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
45 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
46 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
47 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
48 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
49 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
50 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
51 2006 Contreras-Moreira, B. and Collado-Vides, J. (2006). "Comparative Footprinting Of DNA-binding Proteins". Bioinformatics. 22(14):E74-E80   PUBMED: #16873524
52 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
53 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
54 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
55 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
56 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
57 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
58 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
59 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
60 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
61 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
62 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
63 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
64 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
65 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
66 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
67 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
68 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
69 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
70 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    
71 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
72 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
73 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
74 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
75 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    
76 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
77 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
78 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
79 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
80 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    
81 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
82 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
83 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
84 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
85 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
86 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
87 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
88 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
89 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
90 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
91 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
92 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    
93 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
94 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
95 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    
96 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
97 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
98 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
99 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
100 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
101 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
102 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
103 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
104 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
105 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
106 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
107 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
108 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
109 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
110 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
111 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
112 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
113 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
114 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
115 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
116 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
117 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
118 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
119 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
120 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
121 1997 Collado-Vides, J., Huerta, A.M. and Klose, K. (1997). "Three Models Of Gene Regulation in e-coli". Bioinformatics. 1278:72-78    
122 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
123 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
124 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
125 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
126 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
127 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
128 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
129 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
130 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
131 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

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.

Herramientas desarrolladas:

Bioinformatic Systems Standardization


Posdoctoral fellow: Dr. Juan Segura Salazar.

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

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