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+% Encoding: Cp1252
+
+@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}
+}
+