daniel rios garza

Identifiants chercheurs

IdHAL :

daniel-rios-garza

ORCID :

0000-0003-3865-2146

Publications

Article dans une revue (20)

Keystone concept revisited: insights into microbial community dynamics and control Daniel Rios Garza,Didier Gonze,Karoline Faust Nature Reviews Microbiology, 2026, ⟨10.1038/s41579-025-01266-8⟩ Article dans une revue hal-05440960v1
Spatial structure: Shaping the ecology and evolution of microbial communities Marcel Bäcker,Hilje Doekes,Daniel Garza,Jeroen Meijer,Simon van Vlietet al. FEMS Microbiology Reviews, 2026, ⟨10.1093/femsre/fuaf067⟩ Article dans une revue hal-05502139v1
Improving genome-scale metabolic models of incomplete genomes with deep learning Meine D Boer,Chrats Melkonian,Haris Zafeiropoulos,Andreas F Haas,Daniel R Garzaet al. iScience, 2024, 27, ⟨10.1016/j.isci.2024.111349⟩ Article dans une revue hal-04810527v1
Discovery of alternative stable states in a synthetic human gut microbial community Daniel Rios Garza,Bin Liu,Charlotte van de Velde,Xingjian Zhou,Pallabita Sahaet al. Nature Communications, 2024, ⟨10.1101/2024.11.28.625814⟩ Article dans une revue hal-04811996v1
Starvation responses impact interaction dynamics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis Bin Liu,Daniel Rios Garza,Didier Gonze,Anna Krzynowek,Kenneth Simoenset al. The International Society of Microbiologial Ecology Journal, 2023, 17 (11), pp.1940-1952. ⟨10.1038/s41396-023-01501-1⟩ Article dans une revue hal-04485180v1
miaSim: an R/Bioconductor package to easily simulate microbial community dynamics Yu Gao,Yağmur Şimşek,Emma Gheysen,Tuomas Borman,Yi Liet al. Methods in Ecology and Evolution, 2023, 14 (8), pp.1967-1980. ⟨10.1111/2041-210X.14129⟩ Article dans une revue hal-04485172v1
Bacterial Oncotraits Rather than Spatial Organization Are Associated with Dysplasia in Ulcerative Colitis Carlijn Bruggeling,Maarten Te Groen,Daniel Garza,Famke van Heeckeren Tot Overlaer,Joyce Krekelset al. Journal of Crohn's and Colitis, 2023, 17 (11), pp.1870-1881. ⟨10.1093/ecco-jcc/jjad092⟩ Article dans une revue hal-04485176v1
BCG-induced trained immunity enhances acellular pertussis vaccination responses in an explorative randomized clinical trial Joshua Gillard,Bastiaan Blok,Daniel Garza,Prashanna Balaji Venkatasubramanian,Elles Simonettiet al. NPJ vaccines, 2022, 7 (1), pp.21. ⟨10.1038/s41541-022-00438-4⟩ Article dans une revue hal-04485146v1
Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes Daniel Garza,F. von Meijenfeldt,Bram van Dijk,Annemarie Boleij,Martijn Huynenet al. BMC Ecology and Evolution, 2022, 22 (1), pp.101. ⟨10.1186/s12862-022-02052-3⟩ Article dans une revue hal-04485150v1
Optimized bacterial DNA isolation method for microbiome analysis of human tissues Carlijn Bruggeling,Daniel Garza,Soumia Achouiti,Wouter Mes,Bas Dutilhet al. MicrobiologyOpen, 2021, 10 (3), ⟨10.1002/mbo3.1191⟩ Article dans une revue hal-04485137v1
Novel insights from the Plasmodium falciparum sporozoite-specific proteome by probabilistic integration of 26 studies Lisette Meerstein-Kessel,Jeron Venhuizen,Daniel Garza,Nicholas Proellochs,Emma Voset al. PLoS Computational Biology, 2021, 17 (4), pp.e1008067. ⟨10.1371/journal.pcbi.1008067⟩ Article dans une revue hal-04485130v1
A Prioritized and Validated Resource of Mitochondrial Proteins in Plasmodium Identifies Unique Biology Selma van Esveld,Lisette Meerstein-Kessel,Cas Boshoven,Jochem Baaij,Konstantin Barylyuket al. MSphere, 2021, 6 (5), ⟨10.1128/msphere.00614-21⟩ Article dans une revue hal-04485141v1
Metabolic models predict bacterial passengers in colorectal cancer Daniel Garza,Rahwa Taddese,Jakob Wirbel,Georg Zeller,Annemarie Boleijet al. Cancer & metabolism, 2020, 8 (1), pp.3. ⟨10.1186/s40170-020-0208-9⟩ Article dans une revue hal-04485107v1
Growth rate alterations of human colorectal cancer cells by 157 gut bacteria Rahwa Taddese,Daniel Garza,Lilian Ruiter,Marien de Jonge,Clara Belzeret al. Gut microbes, 2020, 12 (1), pp.1799733. ⟨10.1080/19490976.2020.1799733⟩ Article dans une revue hal-04485106v1
Towards predicting the environmental metabolome from metagenomics with a mechanistic model Daniel Garza,Marcel van Verk,Martijn Huynen,Bas Dutilh Nature Microbiology, 2018, 3 (4), pp.456-460. ⟨10.1038/s41564-018-0124-8⟩ Article dans une revue hal-04485093v1
Elucidating genomic gaps using phenotypic profiles Daniel Cuevas,Daniel Garza,Savannah Sanchez,Jason Rostron,Chris Henryet al. F1000Research, 2016, 3, pp.210. ⟨10.12688/f1000research.5140.2⟩ Article dans une revue hal-04485099v1
From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems Daniel Garza,Bas Dutilh Cellular and Molecular Life Sciences, 2015, 72 (22), pp.4287-4308. ⟨10.1007/s00018-015-2004-1⟩ Article dans une revue hal-04485087v1
Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions Bas Dutilh,Cristiane Thompson,Ana Cp Vicente,Michel Marin,Clarence Leeet al. BMC Genomics, 2014, 15 (1), pp.654. ⟨10.1186/1471-2164-15-654⟩ Article dans une revue hal-04485079v1
Population and Genetic Study of Vibrio cholerae from the Amazon Environment Confirms that the WASA-1 Prophage Is the Main Marker of the Epidemic Strain that Circulated in the Region Lena Líllian Canto de Sá Morais,Daniel Rios Garza,Edvaldo Carlos Brito Loureiro,Elivam Rodrigues Vale,Denise Suéllem Amorim de Sousa Santoset al. PLoS ONE, 2013, 8 (11), pp.e81372. ⟨10.1371/journal.pone.0081372⟩ Article dans une revue hal-04485064v1
Genome-Wide Study of the Defective Sucrose Fermenter Strain of Vibrio cholerae from the Latin American Cholera Epidemic Daniel Rios Garza,Cristiane Thompson,Edvaldo Carlos Brito Loureiro,Bas Dutilh,Davi Toshio Inadaet al. PLoS ONE, 2012, 7 (5), pp.e37283. ⟨10.1371/journal.pone.0037283⟩ Article dans une revue hal-04485053v1

Pré-publication, Document de travail (1)

Improving genome-scale metabolic models of incomplete genomes with deep learning Meine Boer,Chrats Melkonian,Haris Zafeiropoulos,Andreas Haas,Daniel Garzaet al. 2024 Pré-publication, Document de travail hal-04485185v1