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  1. Article ; Online: Regulatory promoter architectures in the hands of thermodynamic modelling.

    Collado-Vides, Julio

    Nature reviews. Genetics

    2023  Volume 24, Issue 6, Page(s) 349

    MeSH term(s) Promoter Regions, Genetic ; Transcription Factors/genetics ; Thermodynamics
    Chemical Substances Transcription Factors
    Language English
    Publishing date 2023-02-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 2035157-4
    ISSN 1471-0064 ; 1471-0056
    ISSN (online) 1471-0064
    ISSN 1471-0056
    DOI 10.1038/s41576-023-00578-w
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5474: Show issues Location:
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  2. Article: Missing Links Between Gene Function and Physiology in Genomics.

    Collado-Vides, Julio / Gaudet, Pascale / de Lorenzo, Víctor

    Frontiers in physiology

    2022  Volume 13, Page(s) 815874

    Abstract: Knowledge of biological organisms at the molecular level that has been gathered is now organized into databases, often within ontological frameworks. To enable computational comparisons of annotations across different genomes and organisms, controlled ... ...

    Abstract Knowledge of biological organisms at the molecular level that has been gathered is now organized into databases, often within ontological frameworks. To enable computational comparisons of annotations across different genomes and organisms, controlled vocabularies have been essential, as is the case in the functional annotation classifications used for bacteria, such as MultiFun and the more widely used Gene Ontology. The function of individual gene products as well as the processes in which collections of them participate constitute a wealth of classes that describe the biological role of gene products in a large number of organisms in the three kingdoms of life. In this contribution, we highlight from a qualitative perspective some limitations of these frameworks and discuss challenges that need to be addressed to bridge the gap between annotation as currently captured by ontologies and databases and our understanding of the basic principles in the organization and functioning of organisms; we illustrate these challenges with some examples in bacteria. We hope that raising awareness of these issues will encourage users of Gene Ontology and similar ontologies to be careful about data interpretation and lead to improved data representation.
    Language English
    Publishing date 2022-02-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2564217-0
    ISSN 1664-042X
    ISSN 1664-042X
    DOI 10.3389/fphys.2022.815874
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  3. Book: Integrative approaches to molecular biology

    Collado-Vides, Julio

    [consequence of a meeting held at the Center for Nitrogen Fixation, National Autonomous University of Mexico, Cuernavaca, in Feb. 1994]

    1996  

    Author's details ed. by Julio Collado-Vides
    Keywords Molecular Biology / congresses ; Molekularbiologie
    Subject Molekulare Biologie
    Language English
    Size X, 345 S. : graph. Darst.
    Publisher MIT Press
    Publishing place Cambridge, Mass. u.a.
    Publishing country United States
    Document type Book
    HBZ-ID HT007611290
    ISBN 0-262-03239-2 ; 978-0-262-03239-1
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    1997 A 6345 order for loan Magazin

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  4. Book ; Conference proceedings: Modelling and simulation of gene and cell regulation

    Collado-Vides, Julio

    23.10. - 27.10.95

    (Dagstuhl-Seminar-Report ; 130 = 9543)

    1996  

    Event/congress Seminar on Modelling and Simulation of Complex Environmental Problems (1995, Dagstuhl)
    Author's details Julio Collado-Vides ... (ed.)
    Series title Dagstuhl-Seminar-Report ; 130 = 9543
    Collection
    Language English
    Size 34 S.
    Publisher Geschäftsstelle Schloss Dagstuhl
    Publishing place Saarbrücken
    Publishing country Germany
    Document type Book ; Conference proceedings
    HBZ-ID HT014293237
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    1998 A 10810 order for loan Magazin

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  5. Article: Flexible gold standards for transcription factor regulatory interactions in

    Lara, Paloma / Gama-Castro, Socorro / Salgado, Heladia / Rioualen, Claire / Tierrafría, Víctor H / Muñiz-Rascado, Luis J / Bonavides-Martínez, César / Collado-Vides, Julio

    Frontiers in genetics

    2024  Volume 15, Page(s) 1353553

    Abstract: Post-genomic implementations have expanded the experimental strategies to identify elements involved in the regulation of transcription initiation. Here, we present for the first time a detailed analysis of the sources of knowledge supporting the ... ...

    Abstract Post-genomic implementations have expanded the experimental strategies to identify elements involved in the regulation of transcription initiation. Here, we present for the first time a detailed analysis of the sources of knowledge supporting the collection of transcriptional regulatory interactions (RIs) of
    Language English
    Publishing date 2024-03-05
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2024.1353553
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  6. Article: A Gold Standard for Transcription Factor Regulatory Interactions in

    Lara, Paloma / Gama-Castro, Socorro / Salgado, Heladia / Rioualen, Claire / Tierrafría, Víctor H / Muñiz-Rascado, Luis J / Bonavides-Martínez, César / Collado-Vides, Julio

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Post-genomic implementations have expanded the experimental strategies to identify elements involved in the regulation of transcription initiation. As new methodologies emerge, a natural step is to compare their results with those from established ... ...

    Abstract Post-genomic implementations have expanded the experimental strategies to identify elements involved in the regulation of transcription initiation. As new methodologies emerge, a natural step is to compare their results with those from established methodologies, such as the classic methods of molecular biology used to characterize transcription factor binding sites, promoters, or transcription units. In the case of
    Language English
    Publishing date 2023-12-11
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.02.25.530038
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  7. Article: Genome-Wide Mapping of Transcriptional Regulation and Metabolism Describes Information-Processing Units in

    Ledezma-Tejeida, Daniela / Ishida, Cecilia / Collado-Vides, Julio

    Frontiers in microbiology

    2017  Volume 8, Page(s) 1466

    Abstract: In the face of changes in their environment, bacteria adjust gene expression levels and produce appropriate responses. The individual layers of this process have been widely studied: the transcriptional regulatory network describes the regulatory ... ...

    Abstract In the face of changes in their environment, bacteria adjust gene expression levels and produce appropriate responses. The individual layers of this process have been widely studied: the transcriptional regulatory network describes the regulatory interactions that produce changes in the metabolic network, both of which are coordinated by the signaling network, but the interplay between them has never been described in a systematic fashion. Here, we formalize the process of detection and processing of environmental information mediated by individual transcription factors (TFs), utilizing a concept termed genetic sensory response units (GENSOR units), which are composed of four components: (1) a signal, (2) signal transduction, (3) genetic switch, and (4) a response. We used experimentally validated data sets from two databases to assemble a GENSOR unit for each of the 189 local TFs of
    Language English
    Publishing date 2017-08-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2017.01466
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  8. Article ; Online: Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks.

    Rioualen, Claire / Charbonnier-Khamvongsa, Lucie / Collado-Vides, Julio / van Helden, Jacques

    Current protocols in bioinformatics

    2019  Volume 66, Issue 1, Page(s) e72

    Abstract: Next-generation sequencing (NGS) is becoming a routine approach in most domains of the life sciences. To ensure reproducibility of results, there is a crucial need to improve the automation of NGS data processing and enable forthcoming studies relying on ...

    Abstract Next-generation sequencing (NGS) is becoming a routine approach in most domains of the life sciences. To ensure reproducibility of results, there is a crucial need to improve the automation of NGS data processing and enable forthcoming studies relying on big datasets. Although user-friendly interfaces now exist, there remains a strong need for accessible solutions that allow experimental biologists to analyze and explore their results in an autonomous and flexible way. The protocols here describe a modular system that enable a user to compose and fine-tune workflows based on SnakeChunks, a library of rules for the Snakemake workflow engine. They are illustrated using a study combining ChIP-seq and RNA-seq to identify target genes of the global transcription factor FNR in Escherichia coli, which has the advantage that results can be compared with the most up-to-date collection of existing knowledge about transcriptional regulation in this model organism, extracted from the RegulonDB database. © 2019 by John Wiley & Sons, Inc.
    MeSH term(s) Bacteria/genetics ; Base Sequence ; Chromatin Immunoprecipitation Sequencing/methods ; Genome, Bacterial ; Nucleotide Motifs/genetics ; RNA-Seq ; Software ; User-Computer Interface
    Language English
    Publishing date 2019-02-20
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 1934-340X
    ISSN (online) 1934-340X
    DOI 10.1002/cpbi.72
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  9. Article: Sensory Systems and Transcriptional Regulation in

    Femerling, Georgette / Gama-Castro, Socorro / Lara, Paloma / Ledezma-Tejeida, Daniela / Tierrafría, Víctor H / Muñiz-Rascado, Luis / Bonavides-Martínez, César / Collado-Vides, Julio

    Frontiers in bioengineering and biotechnology

    2022  Volume 10, Page(s) 823240

    Abstract: In free-living bacteria, the ability to regulate gene expression is at the core of adapting and interacting with the environment. For these systems to have a logic, a signal must trigger a genetic change that helps the cell to deal with what implies its ... ...

    Abstract In free-living bacteria, the ability to regulate gene expression is at the core of adapting and interacting with the environment. For these systems to have a logic, a signal must trigger a genetic change that helps the cell to deal with what implies its presence in the environment; briefly, the response is expected to include a feedback to the signal. Thus, it makes sense to think of genetic sensory mechanisms of gene regulation.
    Language English
    Publishing date 2022-02-14
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2719493-0
    ISSN 2296-4185
    ISSN 2296-4185
    DOI 10.3389/fbioe.2022.823240
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  10. Article ; Online: Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes.

    Ledezma-Tejeida, Daniela / Altamirano-Pacheco, Luis / Fajardo, Vicente / Collado-Vides, Julio

    Nucleic acids research

    2019  Volume 47, Issue 13, Page(s) 6656–6667

    Abstract: Transcription factors (TFs) are important drivers of cellular decision-making. When bacteria encounter a change in the environment, TFs alter the expression of a defined set of genes in order to adequately respond. It is commonly assumed that genes ... ...

    Abstract Transcription factors (TFs) are important drivers of cellular decision-making. When bacteria encounter a change in the environment, TFs alter the expression of a defined set of genes in order to adequately respond. It is commonly assumed that genes regulated by the same TF are involved in the same biological process. Examples of this are methods that rely on coregulation to infer function of not-yet-annotated genes. We have previously shown that only 21% of TFs involved in metabolism regulate functionally homogeneous genes, based on the proximity of the gene products' catalyzed reactions in the metabolic network. Here, we provide more evidence to support the claim that a 1-TF/1-process relationship is not a general property. We show that the observed functional heterogeneity of regulons is not a result of the quality of the annotation of regulatory interactions, nor the absence of protein-metabolite interactions, and that it is also present when function is defined by Gene Ontology terms. Furthermore, the observed functional heterogeneity is different from the one expected by chance, supporting the notion that it is a biological property. To further explore the relationship between transcriptional regulation and metabolism, we analyzed five other types of regulatory groups and identified complex regulons (i.e. genes regulated by the same combination of TFs) as the most functionally homogeneous, and this is supported by coexpression data. Whether higher levels of related functions exist beyond metabolism and current functional annotations remains an open question.
    MeSH term(s) Enzymes/genetics ; Enzymes/physiology ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/physiology ; Gene Expression Regulation, Bacterial ; Gene Ontology ; Gene Regulatory Networks/genetics ; Gene Regulatory Networks/physiology ; Metabolic Networks and Pathways ; Regulon/genetics ; Regulon/physiology ; Transcription Factors/physiology
    Chemical Substances Enzymes ; Escherichia coli Proteins ; Transcription Factors
    Language English
    Publishing date 2019-06-08
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkz525
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