All Stories

  1. Prediction of metabolic dynamics through deep learning and high-throughput multiomics data

    Article • May 2025, Cold Spring Harbor Laboratory Press

    Jose Manuel Martí

  2. Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification

    Article • mSystems, April 2025, ASM Journals

    Jose Manuel Martí

  3. Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida

    Article • Communications Biology, April 2025, Springer Science + Business Media

    Jose Manuel Martí

  4. Meta2DB: Curated Shotgun Metagenomic Feature Sets and Metadata for Health State Prediction

    Article • October 2024, Cold Spring Harbor Laboratory Press

    Jose Manuel Martí

  5. GENTANGLE: integrated computational design of gene entanglements

    Article • Bioinformatics, June 2024, Oxford University Press (OUP)

    Jose Manuel Martí

  6. Addressing the dynamic nature of reference data: a new nt database for robust metagenomic classification

    Article • June 2024, Cold Spring Harbor Laboratory Press

    Jose Manuel Martí

  7. Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies

    Article • PLOS One, January 2024, PLOS

    Jose Manuel Martí

  8. PRIMED for the Future: Purposing Raw Intake for Machine Learning-Enabled Detection

    Article • December 2023, Office of Scientific and Technical Information (OSTI)

    Jose Manuel Martí

  9. GENTANGLE: integrated computational design of gene entanglements

    Article • November 2023, Cold Spring Harbor Laboratory Press

    Jose Manuel Martí

  10. Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies

    Article • July 2023, Cold Spring Harbor Laboratory Press

    Jose Manuel Martí

  11. Perspectives for self-driving labs in synthetic biology

    Article • Current Opinion in Biotechnology, February 2023, Elsevier

    Jose Manuel Martí

  12. Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples

    Article • Viruses, December 2022, MDPI AG

    Jose Manuel Martí

  13. Machine learning for metabolic engineering: A review

    Article • Metabolic Engineering, January 2021, Elsevier

    Jose Manuel Martí

  14. Multiomics data collection, visualization, and utilization for guiding metabolic engineering

    Article • October 2020, Cold Spring Harbor Laboratory Press

    Jose Manuel Martí

  15. Metatranscriptomic dynamics after Verticillium dahliae infection and root damage in Olea europaea

    Article • BMC Plant Biology, February 2020, Springer Science + Business Media

    Jose Manuel Martí

  16. Not just BLAST nt: WGS database joins the party

    Article • June 2019, Cold Spring Harbor Laboratory Press

    Jose Manuel Martí

  17. Recentrifuge: robust comparative analysis and contamination removal for metagenomics

    Article • PLoS Computational Biology, April 2019, PLOS

    Jose Manuel Martí

  18. Metagenomic dynamics in Olea europaea after root damage and Verticillium dahliae infection

    Article • February 2019, Cold Spring Harbor Laboratory Press

    Jose Manuel Martí

  19. Time Series Analysis of the Microbiota of Children Suffering From Acute Infectious Diarrhea and Their Recovery After Treatment

    Article • Frontiers in Microbiology, June 2018, Frontiers

    Jose Manuel Martí

  20. Robust Analysis of Time Series in Virome Metagenomics

    Article • January 2018, Springer Science + Business Media

    Jose Manuel Martí

  21. Polar solar panels: Arctic and Antarctic microbiomes display similar taxonomic profiles

    Article • Environmental Microbiology Reports, December 2017, Wiley

    Jose Manuel Martí

  22. Recentrifuge: robust comparative analysis and contamination removal for metagenomics

    Article • September 2017, Cold Spring Harbor Laboratory Press

    Jose Manuel Martí

  23. Microbiota are you sick? Health&disease distilled from the time variability of the human microbiome

    Article • mSystems, March 2017, ASM Journals

    Jose Manuel Martí

  24. Unveiling Bacterial Interactions through Multidimensional Scaling and Dynamics Modeling

    Article • Scientific Reports, December 2015, Nature

    Jose Manuel Martí

  25. Using populations of human and microbial genomes for organism detection in metagenomes

    Article • Genome Research, April 2015, Cold Spring Harbor Laboratory Press

    Jose Manuel Martí

  26. Dark matter merging induced turbulence as an efficient engine for gas cooling

    Article • Monthly Notices of the Royal Astronomical Society, November 2011, Oxford University Press (OUP)

    Jose Manuel Martí

  27. Atmospheric correction algorithm for multiangular satellite measurements in the solar spectrum

    Article • February 2004, SPIE

    Jose Manuel Martí