daniel rios garza

19
Documents
Affiliations actuelles
  • Université Paris-Saclay
  • Procédés biotechnologiques au service de l'environnement (UR PROSE)
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Publications

Publications

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Improving genome-scale metabolic models of incomplete genomes with deep learning

Meine D Boer , Chrats Melkonian , Haris Zafeiropoulos , Andreas F Haas , Daniel R Garza et al.
Article dans une revue hal-04810527 v1

Starvation responses impact interaction dynamics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis

Bin Liu , Daniel Rios Garza , Didier Gonze , Anna Krzynowek , Kenneth Simoens et 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-04485180 v1

miaSim: an R/Bioconductor package to easily simulate microbial community dynamics

Yu Gao , Yağmur Şimşek , Emma Gheysen , Tuomas Borman , Yi Li et al.
Methods in Ecology and Evolution, 2023, 14 (8), pp.1967-1980. ⟨10.1111/2041-210X.14129⟩
Article dans une revue hal-04485172 v1

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 Krekels et al.
Journal of Crohn's and Colitis, 2023, 17 (11), pp.1870-1881. ⟨10.1093/ecco-jcc/jjad092⟩
Article dans une revue hal-04485176 v1

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 Simonetti et al.
NPJ vaccines, 2022, 7 (1), pp.21. ⟨10.1038/s41541-022-00438-4⟩
Article dans une revue hal-04485146 v1

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 Huynen et al.
BMC Ecology and Evolution, 2022, 22 (1), pp.101. ⟨10.1186/s12862-022-02052-3⟩
Article dans une revue hal-04485150 v1

A Prioritized and Validated Resource of Mitochondrial Proteins in Plasmodium Identifies Unique Biology

Selma van Esveld , Lisette Meerstein-Kessel , Cas Boshoven , Jochem Baaij , Konstantin Barylyuk et al.
MSphere, 2021, 6 (5), ⟨10.1128/msphere.00614-21⟩
Article dans une revue hal-04485141 v1

Optimized bacterial DNA isolation method for microbiome analysis of human tissues

Carlijn Bruggeling , Daniel Garza , Soumia Achouiti , Wouter Mes , Bas Dutilh et al.
MicrobiologyOpen, 2021, 10 (3), ⟨10.1002/mbo3.1191⟩
Article dans une revue hal-04485137 v1

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 Vos et al.
PLoS Computational Biology, 2021, 17 (4), pp.e1008067. ⟨10.1371/journal.pcbi.1008067⟩
Article dans une revue hal-04485130 v1

Metabolic models predict bacterial passengers in colorectal cancer

Daniel Garza , Rahwa Taddese , Jakob Wirbel , Georg Zeller , Annemarie Boleij et al.
Cancer & metabolism / Cancer Metab, 2020, 8 (1), pp.3. ⟨10.1186/s40170-020-0208-9⟩
Article dans une revue hal-04485107 v1

Growth rate alterations of human colorectal cancer cells by 157 gut bacteria

Rahwa Taddese , Daniel Garza , Lilian Ruiter , Marien de Jonge , Clara Belzer et al.
Gut microbes, 2020, 12 (1), pp.1799733. ⟨10.1080/19490976.2020.1799733⟩
Article dans une revue hal-04485106 v1

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-04485093 v1

Elucidating genomic gaps using phenotypic profiles

Daniel Cuevas , Daniel Garza , Savannah Sanchez , Jason Rostron , Chris Henry et al.
F1000Research, 2016, 3, pp.210. ⟨10.12688/f1000research.5140.2⟩
Article dans une revue hal-04485099 v1

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-04485087 v1

Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions

Bas Dutilh , Cristiane Thompson , Ana Cp Vicente , Michel Marin , Clarence Lee et al.
BMC Genomics, 2014, 15 (1), pp.654. ⟨10.1186/1471-2164-15-654⟩
Article dans une revue hal-04485079 v1

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 Santos et al.
PLoS ONE, 2013, 8 (11), pp.e81372. ⟨10.1371/journal.pone.0081372⟩
Article dans une revue hal-04485064 v1

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 Inada et al.
PLoS ONE, 2012, 7 (5), pp.e37283. ⟨10.1371/journal.pone.0037283⟩
Article dans une revue hal-04485053 v1