Alise Ponsero

Publications

• iMicrobe: Tools and data-dreaiven discovery platform for the microbiome sciences
• Bacteroides abundance drives birth mode dependent infant gut microbiota developmental trajectories
• Creating Planet Microbe Data Packages
• The Promises and Pitfalls of Machine Learning for Detecting Viruses in Aquatic Metagenomes
• Libra: scalable k-mer–based tool for massive all-vs-all metagenome comparisons
• Libra: Improved Partitioning Strategies for Massive Comparative Metagenomics Analysis
• Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity
• NCBI’s Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements
• High abundances of cyanomyoviruses in marine ecosystems demonstrate ecological relevance
• Planet Microbe Semantic Web Application
• Ten simple rules for organizing a data science workshop
• The dynamic wound microbiome
• Planet Microbe: a platform for marine microbiology to discover and analyze interconnected ‘omics and environmental data
• Molecular response to nitrogen starvation by Frankia alni ACN14a revealed by transcriptomics and functional analysis with a fosmid library in Escherichia coli
• Phage hunters: Computational strategies for finding phages in large-scale ‘omics datasets
• Endoplasmic Reticulum Transport of Glutathione by Sec61 Is Regulated by Ero1 and Bip
• Reexamining the Function of Glutathione in Oxidative Protein Folding and Secretion
• Complete Genome Sequence of Cyanobacterial Siphovirus KBS2A
• Cyanolichen microbiome contains novel viruses that encode genes to promote microbial metabolism
• Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems
• Sources of gut microbiota variation in a large longitudinal Finnish infant cohort
• An extended catalog of integrated prophages in the infant and adult fecal microbiome shows high prevalence of lysogeny
• Comparison of k-mer-based de novo comparative metagenomic tools and approaches
• Evaluation of computational phage detection tools for metagenomic datasets
• Ontology-driven analysis of marine metagenomics
• Human milk oligosaccharide composition is affected by season and parity and associates with infant gut microbiota in a birth mode dependent manner in a Finnish birth cohort
• Paternal and induced gut microbiota seeding complement mother-to-infant transmission
• A cohort study in family triads
• Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients
• Gut microbiota wellbeing index predicts overall health in a cohort of 1000 infants
• Dynamics of gut resistome and mobilome in early life