Publicaciones


# Año Ficha Ligas
1 2017 Keseler, I.M., Mackie, A., Santos-Zavaleta, A., Billington, R., Bonavides-Martínez, C., Caspi, R., Fulcher, C., Gama-Castro, S., Kothari, A., Krummenacker, M., Latendresse, M., Muñíz-Rascado, L., Ong, Q., Paley, S., Peralta-Gil, M., Subhraveti, P., Velázquez-Ramírez, D.A., Weaver, D., Collado-Vides, J., Paulsen, I. and Karp, P.D. (2017). "The EcoCyc Database: Reflecting New Knowledge About Escherichia coli K-12". Nucl Acid Res. 45(D1):D543-D550   PUBMED: #27899573
2 2016 Gama-Castro, S., Salgado, H., Santos-Zavaleta, A., Ledezma-Tejeida, D., Muñíz-Rascado, L., García-Sotelo, J.S., Alquicira-Hernández, K., Martínez-Flores, I., Pannier, L., Castro-Mondragon, J.A., Medina-Rivera, A., Solano-Lira, H., Bonavides-Martínez, C., Pérez-Rueda, E., Alquicira-Hernández, S., Porrón-Sotelo, L., López-Fuentes, A., Hernández-Koutoucheva, A., Del-Moral, V., Rinaldi, F. and Collado-Vides, J. (2016). "RegulonDB Version 9.0: High-level Integration Of Gene Regulation, Coexpression, Motif Clustering And beyond". Nucl Acid Res. 44(D1):D133-D143   PUBMED: #26527724
3 2016 Martínez-Flores, I., Pérez-Morales, D., Sánchez-Pérez, M., Paredes, C.C., Collado-Vides, J., Salgado, H. and Bustamante, V.H. (2016). "In Silico Clustering Of Salmonella Global Gene Expression Data Reveals Novel Genes Co-regulated With the SPI-1 Virulence Genes through Hild". Sci Rep. 6   PUBMED: #27886269
4 2016 Méndez-Cruz, C.F., Medina-Urrea, A. and Sierra, G. (2016). "Unsupervised Morphological Segmentation Based on Affixality Measurements". Pattern Recognitian Letters. 84:127-133   PUBMED: #26698293
5 2016 Moretto, M., Sonego, P., Dierckxsens, N., Brilli, M., Bianco, L., Ledezma-Tejeida, D., Gama-Castro, S., Galardini, M., Romualdi, C., Laukens', K., Collado-Vides, J., Meysman, P. and Engelen, K. (2016). "COLOMBOS V3.0: Leveraging Gene Expression Compendia For Cross- Species Analyses". Nucl Acid Res. 44(D1):D620-D623   PUBMED: #26586805
6 2016 Wang, Q.H., Abdul, S.S., Almeida, L., Ananiadou, S., Balderas-Martinez, Y.I., Batista-Navarro, R., Campos, D., Chilton, L., Chou, H.J., Contreras, G., Cooper, L., Dai, H.J., Ferrell, B., Fluck, J., Gama-Castro, S., George, N., Gkoutos, G., Irin, A.K., Jensen, L.J., Jiménez, S., Jue, T.R., Keseler, I., Madan, S., Matos, S., McQuilton, P., Milacic, M., Mort, M., Natarajan, J., Pafilis, E., Pereira, E., Rao, S., Rinaldi, F., Rothfels, K., Salgado, D., Silva, R.M., Singh, O., Stefancsik, R., Su, C.H., Subramani, S., Tadepally, H.D., Tsaprouni, L., Vasilevsky, N., Wang, X.D., Chatr-Aryamontri, A., Laulederkind, S.J.F., Matis-Mitchell, S., McEntyre, J., Orchard, S., Pundir, S., Rodríguez-Esteban, R., Van Auken, K., Lu, Z.Y., Schaeffer, M., Wu, C.H., Hirschman, L. and Arighi, C.N. (2016). "Overview Of the Interactive Task in BioCreative V". Database-the Journal of Biological Databases and Curation.   PUBMED: #27589961
7 2015 Alvarez-Vasquez, F.J., Freyre-González, J.A., Balderas-Martinez, Y.I., Delgado-Carrillo, M.I. and Collado-Vides, J. (2015). "Mathematical Modeling Of the apo and holo Transcriptional Regulation in Escherichia coli". Molecular Biosystems. 11(4):994-1003   PUBMED: #25683745
8 2015 Frausto-Solís, J., Sánchez-Hernández, J.P., Sánchez-Pérez, M. and García, E.L. (2015). "Golden Ratio Simulated Annealing for Protein Folding Problem". International Journal of Computational Methods. 12(6)    
9 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
10 2014 Gama-Castro, S., Rinaldi, F., López-Fuentes, A., Balderas-Martinez, Y.I., Clematide, S., Ellendorff, T.R., Santos-Zavaleta, A., Marques-Madeira, H. and Collado-Vides, J. (2014). "Assisted Curation of Regulatory Interactions and Growth Conditions of OxyR in e. coli K-12". Database-the Journal of Biological Databases and Curation.   PUBMED: #24903516
11 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
12 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
13 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
14 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
15 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    
16 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
17 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
18 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
19 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
20 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
21 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
22 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
23 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
24 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
25 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
26 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
27 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
28 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
29 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    
30 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
31 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
32 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
33 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
34 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
35 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
36 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
37 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
38 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
39 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
40 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
41 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
42 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
43 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
44 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
45 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
46 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
47 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
48 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    
49 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
50 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
51 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
52 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
53 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
54 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
55 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
56 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
57 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
58 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
59 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
60 2006 Contreras-Moreira, B. and Collado-Vides, J. (2006). "Comparative Footprinting Of DNA-binding Proteins". Bioinformatics. 22(14):E74-E80   PUBMED: #16873524
61 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
62 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
63 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
64 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
65 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
66 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
67 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
68 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
69 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
70 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
71 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
72 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
73 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
74 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
75 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
76 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
77 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
78 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
79 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    
80 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
81 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
82 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
83 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
84 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    
85 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
86 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
87 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
88 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
89 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    
90 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
91 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
92 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
93 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
94 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
95 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
96 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
97 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
98 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
99 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
100 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
101 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    
102 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
103 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
104 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    
105 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
106 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
107 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
108 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
109 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
110 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
111 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
112 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
113 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
114 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
115 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
116 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
117 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
118 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
119 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
120 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
121 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
122 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
123 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
124 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
125 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
126 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
127 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
128 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
129 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
130 1997 Collado-Vides, J., Huerta, A.M. and Klose, K. (1997). "Three Models Of Gene Regulation in e-coli". Bioinformatics. 1278:72-78    
131 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
132 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
133 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
134 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
135 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
136 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
137 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
138 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
139 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
140 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