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1

From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli

Denis Thieffry, Araceli M. Huerta, Ernesto Pérez-Rueda, Julio Collado-Vides

Journal:

Year:

1998

Language:

english

File:

PDF, 111 KB

english, 1998

2

A transformational-grammar approach to the study of the regulation of gene expression

Julio Collado-Vides

Journal:

Journal of Theoretical Biology

Year:

1989

Language:

english

File:

PDF, 1.22 MB

english, 1989

3

Fishing, pollution, climate change, and the long-term decline of coral reefs off Havana, Cuba

Duran, A, Shantz, A A, Burkepile, D E, Collado-Vides, L, Ferrer, V M, Palma, L, Ramos, A, Gonzalez-Díaz, S P

Journal:

Bulletin of Marine Science

Year:

2017

Language:

english

File:

PDF, 15.49 MB

english, 2017

4

Interactive effects of herbivory and substrate orientation on algal community dynamics on a coral reef

Duran, Alain, Collado-Vides, L., Palma, L., Burkepile, D. E.

Journal:

Year:

2018

Language:

english

File:

PDF, 1.49 MB

english, 2018

5

Redefining fundamental concepts of transcription initiation in bacteria

MejÃa-Almonte, Citlalli, Busby, Stephen J. W., Wade, Joseph T., van Helden, Jacques, Arkin, Adam P., Stormo, Gary D., Eilbeck, Karen, Palsson, Bernhard O., Galagan, James E., Collado-Vides, Julio

Journal:

Nature Reviews Genetics

Year:

2020

File:

PDF, 1.94 MB

2020

6

A web site for the computational analysis of yeast regulatory sequences

van Helden, J., Andr�, B., Collado-Vides, J.

Journal:

Year:

2000

Language:

english

File:

PDF, 248 KB

english, 2000

7

Modeling and simulation of metabolic pathways, gene regulation and cell differentiation

Ralf Hofestädt, Michael Mavrovouniotis, Julio Collado-Vides, Markus Löffler

Journal:

Year:

1996

Language:

english

File:

PDF, 444 KB

english, 1996

8

Environmental conditions and transcriptional regulation in Escherichia coli: a physiological integrative approach

Agustino Martínez-Antonio, Heladia Salgado, Socorro Gama-Castro, Rosa María Gutiérrez-Ríos, Verónica Jiménez-Jacinto, Julio Collado-Vides

Journal:

Biotechnology and Bioengineering

Year:

2003

Language:

english

File:

PDF, 364 KB

english, 2003

9

The Elements for a Classification of Units of Genetic Information with a Combinatorial Component

Julio Collado-Vides

Journal:

Journal of Theoretical Biology

Year:

1993

File:

PDF, 875 KB

1993

10

A linguistic representation of the regulation of transcription initiation. II. Distinctive features of sigma 70 promoters and their regulatory binding sites

Julio Collado-Vides

Journal:

Year:

1993

Language:

english

File:

PDF, 1.59 MB

english, 1993

11

A linguistic representation of the regulation of transcription initiation. I. An ordered array of complex symbols with distinctive features

Julio Collado-Vides

Journal:

Year:

1993

Language:

english

File:

PDF, 1.25 MB

english, 1993

12

The growth of random networks as a diffusion process

O. Resendis-Antonio, J. Collado-Vides

Journal:

Physica A: Statistical Mechanics and its Applications

Year:

2004

Language:

english

File:

PDF, 214 KB

english, 2004

13

Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea

Ernesto Pérez-Rueda, Julio Collado-Vides, Lorenzo Segovia

Journal:

Computational Biology and Chemistry

Year:

2004

Language:

english

File:

PDF, 227 KB

english, 2004

14

A syntactic representation of units of genetic information—A syntax of units of genetic information

Julio Collado-Vides

Journal:

Journal of Theoretical Biology

Year:

1991

Language:

english

File:

PDF, 1.63 MB

english, 1991

15

Networks of transcriptional regulation encoded in a grammatical model

Julio Collado-Vides, Rosa Marı́a Gutièrrez-Rı́os, Gemma Bel-Enguix

Journal:

Year:

1998

Language:

english

File:

PDF, 143 KB

english, 1998

16

MORPHOLOGY AND PHOTOSYNTHESIS OF CAULERPA (CHLOROPHYTA) IN RELATION TO GROWTH FORM

Ligia Collado-Vides, Daniel Robledo

Journal:

Journal of Phycology

Year:

1999

Language:

english

File:

PDF, 163 KB

english, 1999

17

From sequence to dynamics: the effects of transcription factor and polymerase concentration changes on activated and repressed promoters

Abel González Pérez, Vladimir Espinosa Angarica, Julio Collado-Vides, Ana Tereza Ribeiro Vasconcelos

Journal:

BMC Molecular Biology

Year:

2009

Language:

english

File:

PDF, 1.94 MB

english, 2009

18

Analysis of the Cellular Functions ofEscherichia coliOperons and Their Conservation inBacillus subtilis

Antoine de Daruvar, Julio Collado-Vides, Alfonso Valencia

Journal:

Journal of Molecular Evolution

Year:

2002

Language:

english

File:

PDF, 117 KB

english, 2002

19

Common History at the Origin of the Position–Function Correlation in Transcriptional Regulators in Archaea and Bacteria

Ernesto Pérez-Rueda, Julio Collado-Vides

Journal:

Journal of Molecular Evolution

Year:

2001

Language:

english

File:

PDF, 276 KB

english, 2001

20

Modeling the Increase and Control ofCaulerpa taxifolia, an Invasive Marine Macroalga

Jennifer L. Ruesink, Ligia Collado-Vides

Journal:

Biological Invasions

Year:

2006

Language:

english

File:

PDF, 409 KB

english, 2006

21

Simulation of the clonal growth of Bostrychia radicans (Ceramiales-Rhodophyta) using Lindenmayer systems

Ligia Collado-Vides, Guillermo Gómez-Alcaraz, Gerardo Rivas-Lechuga, Vinicio Gómez-Gutierrez

Journal:

Year:

1997

Language:

english

File:

PDF, 455 KB

english, 1997

22

Modeling and simulation of gene regulation and metabolic pathways

Julio Collado-Vides, Ralf Hofestädt, Michael Mavrovouniotis, Gerhard Michal

Journal:

Year:

1999

Language:

english

File:

PDF, 55 KB

english, 1999

23

27 Spatiotemporal distribution of abundance and density of calcareous green macroalgae along the florida keys: a synchrony study

L. Collado-vides, L. Rutten, J. Fourqurean

Journal:

Journal of Phycology

Year:

2003

Language:

english

File:

PDF, 498 KB

english, 2003

24

SPATIOTEMPORAL VARIATION OF THE ABUNDANCE OF CALCAREOUS GREEN MACROALGAE IN THE FLORIDA KEYS: A STUDY OF SYNCHRONY WITHIN A MACROALGAL FUNCTIONAL-FORM GROUP

Ligia Collado-Vides, Leanne M. Rutten, James W. Fourqurean

Journal:

Journal of Phycology

Year:

2005

Language:

english

File:

PDF, 750 KB

english, 2005

25

Regulation by transcription factors in bacteria: beyond description

Enrique Balleza, Lucia N. López-Bojorquez, Agustino Martínez-Antonio, Osbaldo Resendis-Antonio, Irma Lozada-Chávez, Yalbi I. Balderas-Martínez, Sergio Encarnación, Julio Collado-Vides

Journal:

FEMS Microbiology Reviews

Year:

2009

Language:

english

File:

PDF, 612 KB

english, 2009

26

The Condition-Dependent Transcriptional Network in Escherichia coli

Karen Lemmens, Tijl De Bie, Thomas Dhollander, Pieter Monsieurs, Bart De Moor, Julio Collado-Vides, Kristof Engelen, Kathleen Marchal

Journal:

Annals of the New York Academy of Sciences

Year:

2009

Language:

english

File:

PDF, 222 KB

english, 2009

27

Minimum information requested in the annotation of biochemical models (MIRIAM)

Novère, Nicolas Le, Finney, Andrew, Hucka, Michael, Bhalla, Upinder S, Campagne, Fabien, Collado-Vides, Julio, Crampin, Edmund J, Halstead, Matt, Klipp, Edda, Mendes, Pedro

Journal:

Nature Biotechnology

Year:

2005

Language:

english

File:

PDF, 216 KB

english, 2005

28

Ichtyotoxic activity of extracts from Mexican marine macroalgae

Graciela De Lara-Isassi, Sergio Álvarez-Hernández, Ligia Collado-Vides

Journal:

Journal of Applied Phycology

Year:

2000

Language:

english

File:

PDF, 60 KB

english, 2000

29

Clonal architecture in marine macroalgae: ecological and evolutionary perspectives

Ligia Collado-Vides

Journal:

Evolutionary Ecology

Year:

2001

Language:

english

File:

PDF, 241 KB

english, 2001

30

Tropical seagrass-associated macroalgae distributions and trends relative to water quality

Ligia Collado-Vides, Valentina G. Caccia, Joseph N. Boyer, James W. Fourqurean

Journal:

Estuarine, Coastal and Shelf Science

Year:

2007

Language:

english

File:

PDF, 1.86 MB

english, 2007

31

Modular analysis of the transcriptional regulatory network of E. coli

Osbaldo Resendis-Antonio, Julio A. Freyre-González, Ricardo Menchaca-Méndez, Rosa M. Gutiérrez-Ríos, Agustino Martínez-Antonio, Cristhian Ávila-Sánchez, Julio Collado-Vides

Journal:

Trends in Genetics

Year:

2005

Language:

english

File:

PDF, 187 KB

english, 2005

32

Transcription unit conservation in the three domains of life: a perspective from Escherichia coli

Gabriel Moreno-Hagelsieb, Victor Treviño, Ernesto Pérez-Rueda, Temple F Smith, Julio Collado-Vides

Journal:

Trends in Genetics

Year:

2001

Language:

english

File:

PDF, 45 KB

english, 2001

33

GETools: gene expression tool for analysis of transcriptome experiments in E. coli

Araceli M. Huerta, Jeremy D. Glasner, Rosa Marı́a Gutiérrez-Rı́os, Fred R. Blattner, Julio Collado-Vides

Journal:

Trends in Genetics

Year:

2002

Language:

english

File:

PDF, 40 KB

english, 2002

34

The comprehensive updated regulatory network ofEscherichia coliK-12

Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Martín Peralta-Gil, Mónica I Peñaloza-Spínola, Agustino Martínez-Antonio, Peter D Karp, Julio Collado-Vides

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 219 KB

english, 2006

35

Automatic reconstruction of a bacterial regulatory network using Natural Language Processing

Carlos Rodríguez-Penagos, Heladia Salgado, Irma Martínez-Flores, Julio Collado-Vides

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 579 KB

english, 2007

36

Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria

Abel D González Pérez, Evelyn González González, Vladimir Espinosa Angarica, Ana Tereza R Vasconcelos, Julio Collado-Vides

Journal:

Year:

2008

Language:

english

File:

PDF, 936 KB

english, 2008

37

Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose inEscherichia coli

Rosa María Gutierrez-Ríos, Julio A Freyre-Gonzalez, Osbaldo Resendis, Julio Collado-Vides, Milton Saier, Guillermo Gosset

Journal:

BMC Microbiology

Year:

2007

Language:

english

File:

PDF, 896 KB

english, 2007

38

Architectural models for apical patterns in Gelidium (Gelidiales, Rhodophyta): hypothesis of growth

Dení Rodríguez Vargas, Ligia Collado-Vides

Journal:

Phycological Research

Year:

1996

Language:

english

File:

PDF, 441 KB

english, 1996

39

Genomic position analyses and the transcription machinery

Ernesto Pérez-Rueda, Jay D. Gralla, Julio Collado-Vides

Journal:

Journal of Molecular Biology

Year:

1998

Language:

english

File:

PDF, 198 KB

english, 1998

40

Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies

J. van Helden, B. André, J. Collado-Vides

Journal:

Journal of Molecular Biology

Year:

1998

Language:

english

File:

PDF, 626 KB

english, 1998

41

Towards a unified grammatical model of σ70 and σ54 bacterial promoters

J. Collado-Vides

Journal:

Year:

1996

Language:

english

File:

PDF, 1.99 MB

english, 1996

42

Distribution of minigenes in the bacteriophage lambda chromosome

Norma-Angélica Oviedo, Heladia Salgado, Julio Collado-Vides, Gabriel Guarneros

Journal:

Year:

2004

Language:

english

File:

PDF, 1.28 MB

english, 2004

43

Sigma70 Promoters in Escherichia coli: Specific Transcription in Dense Regions of Overlapping Promoter-like Signals

Araceli M. Huerta, Julio Collado-Vides

Journal:

Journal of Molecular Biology

Year:

2003

Language:

english

File:

PDF, 1.35 MB

english, 2003

44

Comparative Studies of Transcriptional Regulation Mechanisms in a Group of Eight Gamma-proteobacterial Genomes

Vladimir Espinosa, Abel D. González, Ana T. Vasconcelos, Araceli M. Huerta, Julio Collado-Vides

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 573 KB

english, 2005

45

Internal Versus External Effector and Transcription Factor Gene Pairs Differ in Their Relative Chromosomal Position in Escherichia coli

Sarath Chandra Janga, Heladia Salgado, Julio Collado-Vides, Agustino Martínez-Antonio

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 1.02 MB

english, 2007

46

The Role of DNA-binding Specificity in the Evolution of Bacterial Regulatory Networks

Irma Lozada-Chávez, Vladimir Espinosa Angarica, Julio Collado-Vides, Bruno Contreras-Moreira

Journal:

Journal of Molecular Biology

Year:

2008

Language:

english

File:

PDF, 1.27 MB

english, 2008

47

Identifying global regulators in transcriptional regulatory networks in bacteria

Agustino Martı́nez-Antonio, Julio Collado-Vides

Journal:

Current Opinion in Microbiology

Year:

2003

Language:

english

File:

PDF, 480 KB

english, 2003

48

Structure and evolution of gene regulatory networks in microbial genomes

Sarath Chandra Janga, J. Collado-Vides

Journal:

Research in Microbiology

Year:

2007

Language:

english

File:

PDF, 445 KB

english, 2007

49

Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli

Agustino Martínez-Antonio, Sarath Chandra Janga, Heladia Salgado, Julio Collado-Vides

Journal:

Trends in Microbiology

Year:

2006

Language:

english

File:

PDF, 410 KB

english, 2006

50

Biomechanical properties of Udotea (Halimedales, Chlorophyta) in a Mexican reef lagoon

Collado-Vides, L., DeWreede, R. E., Milligan, K. L. D.

Journal:

Year:

1998

Language:

english

File:

PDF, 308 KB

english, 1998