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+
+@BOOK{Barabasi2002,
+ title = {Linked: The New Science of Networks},
+ publisher = {Perseus Books Group},
+ year = {2002},
+ author = {Albert-L\'{a}szl\'{o} Barab\'{a}si},
+ pages = {256},
+ edition = {First},
+ month = may,
+ isbn = {0738206679},
+ owner = {jfreyre},
+ timestamp = {2008.07.09}
+}
+
+@ARTICLE{Freyre-Gonzalez2008,
+ author = {Julio Augusto Freyre-Gonz\'{a}lez and Jos\'{e} Antonio Alonso-Pav\'{o}n
+ and Luis Gerardo Treviño-Quintanilla and Julio Collado-Vides},
+ title = {Functional architecture of \textit{Escherichia coli}: new insights
+ provided by a natural decomposition approach.},
+ journal = {Genome Biol},
+ year = {2008},
+ volume = {9},
+ pages = {R154},
+ number = {10},
+ month = {Oct},
+ abstract = {ABSTRACT: BACKGROUND: Previous studies have used different methods
+ in an effort to extract the modular organization of transcriptional
+ regulatory networks. However, these approaches are not natural, as
+ they try to cluster strongly connected genes into a module or locate
+ known pleiotropic transcription factors in lower hierarchical layers.
+ Here, we unravel the transcriptional regulatory network of Escherichia
+ coli by separating it into its key elements, thus revealing its natural
+ organization. We also present a mathematical criterion, based on
+ the topological features of the transcriptional regulatory network,
+ to classify the network elements into one of two possible classes:
+ hierarchical or modular genes. RESULTS: We found that modular genes
+ are clustered into physiologically correlated groups validated by
+ a statistical analysis of the enrichment of the functional classes.
+ Hierarchical genes encode transcription factors responsible for coordinating
+ module responses based on general interest signals. Hierarchical
+ elements correlate highly with the previously studied global regulators,
+ suggesting that this could be the first mathematical method to identify
+ global regulators. We identified a new element in transcriptional
+ regulatory networks never described before: intermodular genes. These
+ are structural genes which integrate, at the promoter level, signals
+ coming from different modules, and therefore from different physiological
+ responses. Using the concept of pleiotropy, we have reconstructed
+ the hierarchy of the network and discuss the role of feedforward
+ motifs in shaping the hierarchical backbone of the transcriptional
+ regulatory network. CONCLUSIONS: This study sheds new light on the
+ design principles underpinning the organization of transcriptional
+ regulatory networks, showing a novel nonpyramidal architecture comprised
+ of independent modules globally governed by hierarchical transcription
+ factors, whose responses are integrated by intermodular genes.},
+ doi = {10.1186/gb-2008-9-10-r154},
+ owner = {jfreyre},
+ pii = {gb-2008-9-10-r154},
+ pmid = {18954463},
+ timestamp = {2008.10.29},
+ url = {http://dx.doi.org/10.1186/gb-2008-9-10-r154}
+}
+
+@MISC{Freyre-Gonzalez2005,
+ author = {Julio A. Freyre-Gonz\'{a}lez and Jos\'{e} A. Alonso-Pav\'{o}n and
+ Daniel V\'{a}zquez-Hernandez and Mario Sandoval-Calderon and Mariana
+ Matus-Garc\'{\i}a and Ortega-del Vecchyo, Diego and Julio Collado-Vides},
+ title = {Modular and hierarchical organization of the transcriptional regulatory
+ network of \textit{Escherichia coli} K-12},
+ howpublished = {5th International Workshop on Bioinformatics and Systems Biology,
+ Poster Session, Berlín, Alemania},
+ month = {August},
+ year = {2005},
+ abstract = {There are strong arguments that support the idea of modular organization
+ in the cell [3]. A module is defined as a group of correlated elements
+ that cooperate in a specific cellular function [3,1]. In genetic
+ networks, these modules are integrated by transcription factors (TFs)
+ and genes that act coordinately when specific stimuli are present.
+ In biological networks there exist global TFs that interact with
+ several elements of many modules. This makes difficult or impossible
+ to classify those TFs into a single module. Consequently, we may
+ classify the network’s elements into two groups: elements that belong
+ to modules (genes and local TFs, which will hereafter be called modular
+ elements), and elements that coordinate such modules in a hierarchical
+ fashion (global TFs and sigma factors, which will hereafter be called
+ control elements). This suggests that a methodology that will allow
+ for the classification of the network’s genes in one of the aforementioned
+ groups is required.
+
+ Recently, topological analyses have suggested the existence of hierarchical
+ modularity in the transcriptional regulatory network (TRN) of E.
+ coli [2,6,5]. Nevertheless, these studies have neglected the importance
+ of classifying genes in modular and control elements, as well as
+ the existence of feedback circuits among them. Such feedback circuits
+ could be interpreted as a mechanism by which control elements retrieve
+ information about the status of genes in modules and, based on this
+ feedback signal, generate decisions about the fate of the cell.
+
+ Assuming these hypotheses, in our laboratory, we are working on an
+ algorithm to propose a hierarchical structure of the TRN:
+
+ 1. Using data from RegulonDB [7,4] we will decompose the network,
+ through the analysis of the node degree and clustering coefficient
+ distribution, into the aforementioned groups and temporally remove
+ the control elements.
+
+ 2. Using Monica Riley’s gene functional assignations [8] we will analyze
+ the modules to determine whether they are physiologically correlated
+ or not.
+
+ 3. Finally, we will add the removed control elements to infer the
+ hierarchical structure of the TRN.
+
+ On this poster we will show the results obtained from applying this
+ methodology to the TRN of E. coli.},
+ owner = {jfreyre},
+ timestamp = {2008.11.09}
+}
+
+@ARTICLE{Gottesman1984,
+ author = {S. Gottesman},
+ title = {Bacterial regulation: global regulatory networks},
+ journal = {Annu Rev Genet},
+ year = {1984},
+ volume = {18},
+ pages = {415--441},
+ doi = {10.1146/annurev.ge.18.120184.002215},
+ keywords = {Aerobiosis; Anaerobiosis; Bacterial Proteins; Base Sequence; Cyclic
+ AMP; DNA Repair; Energy Metabolism; \textit{Escherichia coli}; Gene
+ Expression Regulation; Glucose; Heat-Shock Proteins; Nitrogen; Operon;
+ Phosphate; Receptors, Cyclic AMP; Repressor Proteins; s},
+ owner = {jfreyre},
+ pmid = {6099091},
+ timestamp = {2008.02.05},
+ url = {http://dx.doi.org/10.1146/annurev.ge.18.120184.002215}
+}
+
+@ARTICLE{Griffith2002,
+ author = {Kevin L Griffith and Ishita M Shah and Todd E Myers and Michael C
+ O'Neill and Richard E Wolf},
+ title = {Evidence for ``pre-recruitment'' as a new mechanism of transcription
+ activation in \textit{Escherichia coli}: the large excess of SoxS
+ binding sites per cell relative to the number of SoxS molecules per
+ cell},
+ journal = {Biochem Biophys Res Commun},
+ year = {2002},
+ volume = {291},
+ pages = {979--986},
+ number = {4},
+ month = {Mar},
+ abstract = {In response to the oxidative stress imposed by redox-cycling compounds
+ like paraquat, \textit{Escherichia coli} induces the synthesis of
+ SoxS, which then activates the transcription of approximately 100
+ genes. The DNA binding site for SoxS-dependent transcription activation,
+ the "soxbox," is highly degenerate, suggesting that the genome contains
+ a large number of SoxS binding sites. To estimate the number of soxboxes
+ in the cell, we searched the \textit{E. coli} genome for SoxS binding
+ sites using as query sequence the previously determined optimal SoxS
+ binding sequence. We found approximately 12,500 sequences that match
+ the optimal binding sequence under the conditions of our search;
+ this agrees with our previous estimate, based on information theory,
+ that a random sequence the size of the \textit{E. coli} genome contains
+ approximately 13,000 soxboxes. Thus, fast-growing cells with 4-6
+ genomes per cell have approximately 65,000 soxboxes. This large number
+ of potential SoxS binding sites per cell raises the interesting question
+ of how SoxS distinguishes between the functional soxboxes located
+ within the promoters of target genes and the plethora of equivalent
+ but nonfunctional binding sites scattered throughout the chromosome.
+ To address this question, we treated cells with paraquat and used
+ Western blot analysis to determine the kinetics of SoxS accumulation
+ per cell; we also determined the kinetics of SoxS-activated gene
+ expression. The abundance of SoxS reached a maximum of 2,500 molecules
+ per cell 20 min after induction and gradually declined to approximately
+ 500 molecules per cell over the next 1.5 h. Given that activation
+ of target gene expression began almost immediately and given the
+ large disparity between the number of SoxS molecules per cell, 2,500,
+ and the number of SoxS binding sites per cell, 65,000, we infer that
+ SoxS is not likely to activate transcription by the usual "recruitment"
+ pathway, as this mechanism would require a number of SoxS molecules
+ similar to the number of soxboxes. Instead, we propose that SoxS
+ first interacts in solution with RNA polymerase and then the binary
+ complex scans the chromosome for promoters that contain a soxbox
+ properly positioned and oriented for transcription activation. We
+ name this new pathway "pre-recruitment."},
+ doi = {10.1006/bbrc.2002.6559},
+ institution = {Department of Biological Sciences, University of Maryland Baltimore
+ County, Baltimore, Maryland 21250, USA.},
+ keywords = {Bacterial Proteins; Binding Sites; Blotting, Western; Cell Division;
+ DNA-Binding Proteins; \textit{Escherichia coli}; \textit{Escherichia
+ coli} Proteins; Gene Expression Regulation, Bacterial; Genome, Bacterial;
+ Kinetics; Numerical Analysis, Computer-Assisted; Oxidative Stress;
+ Paraquat; Protein Transport; Trans-Activation (Genetics); Trans-Activators;
+ Transcription Factors},
+ owner = {jfreyre},
+ pii = {S0006291X02965599},
+ pmid = {11866462},
+ timestamp = {2008.02.05},
+ url = {http://dx.doi.org/10.1006/bbrc.2002.6559}
+}
+
+@ARTICLE{Hartwell1999,
+ author = {L. H. Hartwell and J. J. Hopfield and S. Leibler and A. W. Murray},
+ title = {From molecular to modular cell biology},
+ journal = {Nature},
+ year = {1999},
+ volume = {402},
+ pages = {C47--C52},
+ number = {6761 Suppl},
+ month = {Dec},
+ abstract = {Cellular functions, such as signal transmission, are carried out by
+ 'modules' made up of many species of interacting molecules. Understanding
+ how modules work has depended on combining phenomenological analysis
+ with molecular studies. General principles that govern the structure
+ and behaviour of modules may be discovered with help from synthetic
+ sciences such as engineering and computer science, from stronger
+ interactions between experiment and theory in cell biology, and from
+ an appreciation of evolutionary constraints.},
+ doi = {10.1038/35011540},
+ institution = {Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA.},
+ keywords = {Action Potentials; Evolution; Forecasting; Models, Biological; Molecular
+ Biology},
+ owner = {jfreyre},
+ pmid = {10591225},
+ timestamp = {2008.02.05},
+ url = {http://dx.doi.org/10.1038/35011540}
+}
+
+@ARTICLE{Keseler2005,
+ author = {Ingrid M Keseler and Julio Collado-Vides and Socorro Gama-Castro
+ and John Ingraham and Suzanne Paley and Ian T Paulsen and Martín
+ Peralta-Gil and Peter D Karp},
+ title = {EcoCyc: a comprehensive database resource for \textit{Escherichia
+ coli}},
+ journal = {Nucleic Acids Res},
+ year = {2005},
+ volume = {33},
+ pages = {D334--D337},
+ number = {Database issue},
+ month = {Jan},
+ abstract = {The EcoCyc database (http://EcoCyc.org/) is a comprehensive source
+ of information on the biology of the prototypical model organism
+ \textit{Escherichia coli} K12. The mission for EcoCyc is to contain
+ both computable descriptions of, and detailed comments describing,
+ all genes, proteins, pathways and molecular interactions in E.coli.
+ Through ongoing manual curation, extensive information such as summary
+ comments, regulatory information, literature citations and evidence
+ types has been extracted from 8862 publications and added to Version
+ 8.5 of the EcoCyc database. The EcoCyc database can be accessed through
+ a World Wide Web interface, while the downloadable Pathway Tools
+ software and data files enable computational exploration of the data
+ and provide enhanced querying capabilities that web interfaces cannot
+ support. For example, EcoCyc contains carefully curated information
+ that can be used as training sets for bioinformatics prediction of
+ entities such as promoters, operons, genetic networks, transcription
+ factor binding sites, metabolic pathways, functionally related genes,
+ protein complexes and protein-ligand interactions.},
+ doi = {10.1093/nar/gki108},
+ institution = {SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA.},
+ keywords = {Computational Biology; Databases, Genetic; \textit{Escherichia coli}
+ K12; \textit{Escherichia coli} Proteins; Gene Expression Regulation,
+ Bacterial; Genome, Bacterial; Genomics; Software; User-Computer Interface},
+ owner = {jfreyre},
+ pii = {33/suppl_1/D334},
+ pmid = {15608210},
+ timestamp = {2008.02.05},
+ url = {http://dx.doi.org/10.1093/nar/gki108}
+}
+
+@ARTICLE{Leskovec2008,
+ author = {Jure Leskovec and Eric Horvitz},
+ title = {Planetary-scale views on an instant-messaging network},
+ year = {2008},
+ month = mar,
+ abstract = {We present a study of anonymized data capturing a month of high-level
+ communication activities within the whole of the Microsoft Messenger
+ instant-messaging system. We examine characteristics and patterns
+ that emerge from the collective dynamics of large numbers of people,
+ rather than the actions and characteristics of individuals. The dataset
+ contains summary properties of 30 billion conversations among 240
+ million people. From the data, we construct a communication graph
+ with 180 million nodes and 1.3 billion undirected edges, creating
+ the largest social network constructed and analyzed to date. We report
+ on multiple aspects of the dataset and synthesized graph. We find
+ that the graph is well-connected and robust to node removal. We investigate
+ on a planetary-scale the oft-cited report that people are separated
+ by ``six degrees of separation'' and find that the average path length
+ among Messenger users is 6.6. We also find that people tend to communicate
+ more with each other when they have similar age, language, and location,
+ and that cross-gender conversations are both more frequent and of
+ longer duration than conversations with the same gender.},
+ eprint = {arXiv:0803.0939v1 [physics.soc-ph]},
+ keywords = {Physics - Physics and Society},
+ owner = {jfreyre},
+ timestamp = {2008.07.01},
+ url = {http://arxiv.org/abs/0803.0939}
+}
+
+@BOOK{Lipschutz1986,
+ title = {Estructura de Datos},
+ publisher = {Mcgraw-Hill},
+ year = {1986},
+ author = {Seymour Lipschutz},
+ pages = {352},
+ series = {Serie Schaum},
+ month = dec,
+ isbn = {0070380015},
+ owner = {jfreyre},
+ timestamp = {2008.07.09}
+}
+
+@INCOLLECTION{Marconi1967,
+ author = {Guglielmo Marconi},
+ title = {Wireless Telegraphic Communication},
+ booktitle = {Physics 1901--1921},
+ publisher = {Elsevier Publishing Company},
+ year = {1967},
+ series = {Nobel Lectures},
+ pages = {196--222},
+ address = {Amsterdam},
+ owner = {jfreyre},
+ timestamp = {2008.06.30}
+}
+
+@INCOLLECTION{Neidhardt1996,
+ author = {Neidhardt, F. C. and Savageau, M.},
+ title = {Regulation beyond the operon},
+ booktitle = {Escherichia coli and Salmonella: Cellular and Molecular Biology},
+ publisher = {American Society for Microbiology},
+ year = {1996},
+ editor = {Neidhardt, F. C.},
+ pages = {1310--1324},
+ address = {Washington D.C.},
+ edition = {Second},
+ owner = {jfreyre},
+ timestamp = {2008.04.18}
+}
+
+@BOOK{Nelson2000,
+ title = {Lehninger Principles of Biochemistry},
+ publisher = {W. H. Freeman},
+ year = {2000},
+ author = {David L. Nelson and Michael M. Cox},
+ pages = {1200},
+ edition = {Third},
+ month = feb,
+ isbn = {1572599316},
+ owner = {jfreyre},
+ timestamp = {2008.07.25}
+}
+