My activities

Current research interests

Viral hunting in metagenomes

Understanding the role and distribution of viruses in ecosystems is critical and metagenomics offers new avenues. In order to explore the viral biodiversity and ecology, a number of bioinformatic tools perform a high-level taxonomic (viral or cellular origin) assignment of metagenomic sequences. These tools aim to collect all viral sequences in a metagenome and to help the discovery of new viral groups. While many tools rely on references databases, new approaches using machine learning and pattern detection techniques have been suggested. Indeed, machine learning model can be trained to identify a set of features that signals a viral origin to generalize the identification of all viral sequences. As users of these tools, we aim to explore the promise and current limitations of viral detection in metagenomic datasets.

Read Schackard, Graham, Ponsero and Hurwitz (2023) Evaluation of Computational Phage Detection Tools for Metagenomic Datasets, Frontiers in Microbiology
Read Ponsero et al. (2021) Cyanolichen microbiome contains novel viruses that encode genes to promote microbial metabolism, ISME communication
Read Ponsero and Hurwitz (2019) The promises and pitfalls of machine learning for detecting viruses in aquatic metagenomes, Frontiers in Microbiology
Read Hurwitz , Ponsero, Thornton, U’Ren (2017) Phage Hunters: computational strategies for finding phages in large-scale ‘omics datasets, Virus research (Review article)

FAIR principle applied to metagenomic datasets

Oceanographic research cruises are collaborative efforts providing critical physical, chemical, and biological data (‘omics data and non-omics measurements). These research expeditions span across a broad array of disciplines; they are critical to investigating the interplay between biological, geological and chemical processes in the ocean.
Importantly, although scientists carefully curate and share their data with collaborators to advance individual studies and publications, no systematic, unifying framework currently exists to integrate ‘omics data with physical, geological, geochemical and biological datasets standardly used by the broader geoscience community.
In this context, the development of resources to promote the publication of oceanic ‘omics datasets, along with their physio-chemical information, is critical.
We developed Planet Microbe, a web platform for the integration of ‘omics datasets in their broader environmental context. Moreover, the project intends to provide community tools to support the publication and analysis of new oceanic datasets. Modern data publication requires the user to meet FAIR data standards to ensure data are Findable Accessible, Interoperable, and Reusable (FAIR); however, few tools are currently available for the user to ensure the data meet these important standards. Planet Microbe has the goal to provide tools to evaluate private datasets against these standards and promote the integration of new data in standard data repositories.

Read Ponsero et al. (2021) Planet Microbe: a platform for marine microbiology to discover and analyze interconnected ‘omics and environmental data, NAR
Read Blumberg, Ponsero et al. (2021) Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems, Frontiers in Microbiology
Discover Planet Microbe
Read Youens-Clark, Bomhoff, Ponsero et al. (2020) iMicrobe: Tools and data-driven discovery platform for the microbiome sciences, Gigascience
Discover iMicrobe

Skill set

Computational skills

Python, Perl, R and Shiny app development, Java programming and Bash scripting. Highperformance clusters pipelines parallelization. Big data handling and analysis. Relational and document-based databases modeling and use. Notions of web-development.

Data science

Supervised and unsupervised traditional machine learning methods, data visualization, data curation, data interoperability, application of FAIR data principles..

Bioinformatics

Main metagenomics analysis and annotation methods, kmer-based metagenomics analytics, multi-omics statistical integration.

Experimental skills

Main techniques of molecular genetics, molecular biology and microbiology (bacterial and fungi yeasts). Yeast genetics techniques (dissection, mating…). Handling and use of radioactive labels.

Language

French (mothertongue), English (fluent), Italian (fluent), Spanish (fluent), Finnish (beginner)

Litterary translations

Published translations (from English to French) of science-fiction works co-realised with Erwann Perchoc.

Nancy Kress, Le Nexus du Dr Erdmann, 2016, (novella), éd. du Bélial

Daryl Gregory, « Dead Horse Point », 2014 (short story), Bifrost#74

Eric Brown, « Exorciser ses fantômes », 2011 (short story), Bifrost#63

Outreach

Scientific heritage

Short project in collaboration with the CNB (cercle Naturaliste Brestois) to evaluate and index the academic herbarium from the University of Brest (UBO). The herbarium, compting more than 30.000 specimens was collected by Claude and Mireille Moreau at the time of the University's creation around 1960. The project allowed to shed light on the critical condition of some collections, left unsuppervised for years.
The conclusion of this inventory work was published in a botanical journal (see below) and presented to a conference on scientific heritage (colloque Patrimoine scientifique en Bretagne, 2009).

Read Sawtschuk, Ponsero, Andé-Ormod (2009) Les herbiers du massif armoricain, N°22 E.R.I.C.A. (Echo régional pour l’inventaire et la conservation Armoricaine) (in French)

Science and cinema

Having a global interest in science representation in cinema and litterature, I like to explore how art influence biology and vice-versa.

This published article explore the representation of the "monsters" in science-fiction and its evolution through history and biological advances.
J-S Steyer, A Ponsero and R. Lehoucq. (2019) “Les monstres de la science-fiction : des morphologies et des gènes hors-norme”, Bifrost magazine n°93 (in French)

Open Source ecologie France

From 2015 to 2018, I was a volunteer in charge of communication and outreach for Open Source Ecologie France. I helped the communication and outreach about the development of open source hardware in the context of climate change. I also participated in the communication and management around the “Solar-OSE” crowdfunding project (raised 8000E in 2015).

Blog of Open Source Ecologie France (in French)

Downloads

Resume

You can find more information on my education and scientific experiences in my short resume or in my Curriculum vitae. References are availables for inquiries. Please contact me for more information.

Curriculum vitae
OrcID profile
Google Scholar profile
ResearchGate profile

Protocol.io and Github

Browse my protocols published on Protocols.io and my scripts on Github !

Protocols.io
Github

Professional portfolio

About me