A5034245473- Gut microbiota and health
- Biomedical Text Mining and Ontologies
- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- Scientific Computing and Data Management
- Metabolomics and Mass Spectrometry Studies
- Gene Regulatory Network Analysis
- Natural Language Processing Techniques
- Topic Modeling
- Biofuel production and bioconversion
- Genomics and Phylogenetic Studies
- Computational Drug Discovery Methods
- Evolutionary Algorithms and Applications
- Nematode management and characterization studies
- Mycorrhizal Fungi and Plant Interactions
- Business Process Modeling and Analysis
- Bayesian Methods and Mixture Models
- Research Data Management Practices
- Microbial Community Ecology and Physiology
- Soil Carbon and Nitrogen Dynamics
- Geochemistry and Geologic Mapping
- Clostridium difficile and Clostridium perfringens research
- Semantic Web and Ontologies
- Plant Pathogens and Resistance
- Metaheuristic Optimization Algorithms Research
Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria
2019-2023
Universidad Politécnica de Madrid
2018-2023
Centre for Plant Biotechnology and Genomics
2014-2020
Centro Nacional de Biotecnología
2018-2020
Consejo Superior de Investigaciones Científicas
2018-2020
Universidad Carlos III de Madrid
2003-2014
Spanish National Cancer Research Centre
2008
Abstract Several studies have shown that neither the formal representation nor functional requirements of genome-scale metabolic models (GEMs) are precisely defined. Without a consistent standard, comparability, reproducibility, and interoperability across groups software tools cannot be guaranteed. Here, we present memote ( https://github.com/opencobra/memote ) an open-source containing community-maintained, standardized set me tabolic mo del te sts. The tests cover range aspects from...
Synthetic microbial communities begin to be considered as promising multicellular biocatalysts having a large potential replace engineered single strains in biotechnology applications, pharmaceutical, chemical and living architecture sectors. In contrast strain engineering, the effective high-throughput analysis engineering of consortia face lack knowledge, tools well-defined workflows. This manuscript contributes fill this important gap with framework, called FLYCOP (FLexible sYnthetic...
Construction and analysis of genome-scale metabolic models (GEMs) is a well-established systems biology approach that can be used to predict growth phenotypes. The ability GEMs produce mechanistic insight into microbial ecological processes makes them appealing tools open range exciting opportunities in microbiome research.
Abstract Motivation Microbial communities influence their environment by modifying the availability of compounds, such as nutrients or chemical elicitors. Knowing microbial composition a site is therefore relevant to improve productivity health. However, sequencing facilities are not always available, may be prohibitively expensive in some cases. Thus, it would desirable computationally predict from more accessible, easily-measured features. Results Integrating deep learning techniques with...
Soil microorganisms are in constant interaction with plants, and these interactions shape the composition of soil bacterial communities by modifying their environment. However, little is known about relationship between native plants present extreme environments that not affected human intervention. Using high-throughput sequencing combination random forest co-occurrence network analyses, we compared inhabiting rhizosphere surrounding (RSS) corresponding bulk (BS) 21 plant species organized...
Agricultural management influences the soil ecosystem by affecting its physicochemical properties, residues of pesticides and microbiome. As vineyards grow crops with highest incidence pesticides, aim this study was to evaluate impact conventional sustainable systems from DOP Ribeiro on soil’s condition. Samples soils under three different were collected, main properties evaluated. A selection 50 investigated liquid chromatography tandem mass spectrometry. The bacterial fungal microbiomes...
The EcID database (Escherichia coli Interaction Database) provides a framework for the integration of information on functional interactions extracted from following sources: EcoCyc (metabolic pathways, protein complexes and regulatory information), KEGG pathways), MINT IntAct (protein interactions). It also includes two E. high-throughput pull-down experiments potential literature using web services associated to iHOP text-mining system. Additionally, incorporates results various prediction...
Maintenance of soil health is foremost importance to sustain and increase crop productivity, while meeting the demand a rising global population. Soil microbiome gaining increasing attention as modulator health. Microbial communities confer traits living organism, which functions holistically conforms part plant holobiont, reassembling human-gut axis. Novel strategies in biostimulant development advocate for modulation native reinforcement microbial networking outpace pathogen inclusion....
Recent microbiome dynamics studies highlight the current inability to predict effects of external perturbations on complex microbial populations. To do so would be particularly advantageous in fields such as medicine, bioremediation or industrial scenarios.MDPbiome statistically models longitudinal metagenomics samples undergoing a Markov Decision Process (MDP). Given starting composition, our MDPbiome system suggests sequence perturbation(s) that will engineer goal state, for example,...
Analysis of microbiome dynamics would allow elucidation patterns within microbial community evolution under a variety biologically or economically important circumstances; however, this is currently hampered in part by the lack rigorous, formal, yet generally-applicable approaches to discerning distinct configurations complex populations. Clustering define “community state-types” at population-scale are widely used, though not standardized. Similarly, variations state-type well documented,...
Understanding the effectiveness and potential mechanism of action agricultural biological products under different soil profiles crops will allow more precise product recommendations based on local conditions ultimately result in increased crop yield. This study aimed to use bulk rhizosphere microbial composition structure evaluate effect a Bacillus amyloliquefaciens inoculant (strain QST713) potatoes explore its relationship with We implemented next-generation sequencing (NGS)...
Potato ( Solanum tuberosum L. ) is considered one of the most widely consumed crops worldwide, due to its high yield and nutritional profile, climate change-related environmental threats increasing food demand. This scenario highlights need sustainable agricultural practices enhance potato productivity, while preserving maintaining soil health. Plant growth-promoting bacteria (PGPB) stimulate crop production through biofertilization mechanisms with low impact. For instance, PGPB promote...
Background Molecular biology is currently facing the challenging task of functionally characterizing proteome. The large number possible protein-protein interactions and complexes, variety environmental conditions cellular states in which these can be reorganized, multiple ways a protein influence function others, requires development experimental computational approaches to analyze predict functional associations between proteins as part their activity interactome. Methodology/Principal...
Abstract Background : There are few large longitudinal microbiome studies, and fewer that include controlled, well-annotated perturbations between sampling-points. Thus, there opportunities to employ data-driven computational analyses of perturbed microbial communities over time. Results Our novel system simulates the dynamics under using genome-scale metabolic models (GEMs). Perturbations modifications a) nutrients available in medium, allowing modelling prebiotics; and/or b) microorganisms...
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Determining if a group of proteins are functionally associated among themselves is an open problem in molecular biology. Within our long term goal applying Genetic Programming (GP) to this domain, paper evaluates the feasibility GP predict given pair interacts. has been chosen because its potential flexibility many aspects, such as definition operations. In paper, if-unknown operation defined, which semantically most appropriate domain for handling missing values. We have also used Tarpeian...
The grammatical structures scholars use to express their assertions are intended convey various degrees of certainty or speculation. Prior studies have suggested a variety categorization systems for scholarly certainty; however, these not been objectively tested validity, particularly with respect representing the interpretation by reader, rather than intention author. In this study, we series questionnaires determine how researchers classify assertions, using three distinct classification...
Biological pathways are important elements of systems biology and in the past decade, an increasing number pathway databases have been set up to document growing understanding complex cellular processes. Although more genome-sequence data becoming available, a large fraction it remains functionally uncharacterized. Thus, is be able predict mapping poorly annotated proteins original models. Results: We developed Relational Learning-based Extension (RLE) system investigate membership through...
Societal Impact Statement Winegrape production is an essential cultural heritage and economic engine of many regions the world. Regenerative management, which gaining traction with industry consumers alike, relies on soil biodiversity for agroecosystem function, reducing external inputs increasing ecosystem resilience to climate change. We evaluated effects no‐till sheep integration vineyard function. No‐till had stronger microbial diversity, while grazing stimulated functioning. By...
The analysis of microbiome dynamics would allow us to elucidate patterns within microbial community evolution; however, state-transition have been scarcely studied. This is in part because a necessary first-step such analyses has not well-defined: how deterministically describe microbiome’s ”state”. Clustering states widely studied, although no standard concluded yet. We propose generic, domain-independent and automatic procedure determine reliable set sub-states specific dataset, with...