All Stories

  1. Draft assemblies for three geographically distinct isolates of the human-infecting microsporidium Encephalitozoon intestinalis

    Article • Microbiology Resource Announcements, November 2025, ASM Journals

    Dr Jean-François Pombert

  2. Comparative Genomics of Chloropicon primus and Chloropicon roscoffensis Provide Insights into the Evolutionary Dynamics and Ecological Success of These Tiny Green Algae in Marine Environments

    Article • Genome Biology and Evolution, July 2025, Oxford University Press (OUP)

    Dr Jean-François Pombert

  3. Comparative plastome and mitogenome analyses indicate that the marine prasinophyte green algae Pycnococcus provasolii and Pseudoscourfieldia marina (Pseudoscourfieldiophyceae class nov., Chlorophyta) represent morphotypes of the same species

    Article • Journal of Phycology, July 2024, Wiley

    Dr Jean-François Pombert

  4. SYNY: a pipeline to investigate and visualize collinearity between genomes

    Article • May 2024, Cold Spring Harbor Laboratory Press

    Dr Jean-François Pombert

  5. Near chromosome–level genome assembly of the microsporidium Hamiltosporidium tvaerminnensis

    Article • G3 Genes Genomes Genetics, August 2023, Oxford University Press (OUP)

    Dr Jean-François Pombert

  6. Near chromosome-level genome assembly of the microsporidiumHamiltosporidium tvaerminnensis

    Article • June 2023, Cold Spring Harbor Laboratory Press

    Dr Jean-François Pombert

  7. The Rad9–Rad1–Hus1 DNA Repair Clamp is Found in Microsporidia

    Article • Genome Biology and Evolution, April 2022, Oxford University Press (OUP)

    Dr Jean-François Pombert

  8. A new microsporidian parasite, Ordospora pajunii sp. nov (Ordosporidae), of Daphnia longispina highlights the value of genomic data for delineating species boundaries

    Article • Journal of Eukaryotic Microbiology, March 2022, Wiley

    Dr Jean-François Pombert

  9. 3DFI: a pipeline to infer protein function using structural homology

    Article • Bioinformatics Advances, January 2021, Oxford University Press (OUP)

    Dr Jean-François Pombert

  10. Microsporidia with Vertical Transmission Were Likely Shaped by Nonadaptive Processes

    Article • Genome Biology and Evolution, December 2019, Oxford University Press (OUP)

    Dr Jean-François Pombert

  11. A streamlined and predominantly diploid genome in the tiny marine green alga Chloropicon primus

    Article • Nature Communications, September 2019, Springer Science + Business Media

    Dr Jean-François Pombert

  12. The bacteriocin from the prophylactic candidate Streptococcus suis 90-1330 is widely distributed across S. suis isolates and appears encoded in an integrative and conjugative element

    Article • PLOS One, April 2019, PLOS

    Dr Jean-François Pombert

  13. Complete Genome Sequence of Vitreoscilla sp. Strain C1, Source of the First Bacterial Hemoglobin

    Article • Microbiology Resource Announcements, August 2018, ASM Journals

    Dr Jean-François Pombert

  14. Complete Genome Sequences of the Potential Zoonotic Pathogens Staphylococcus felis and Staphylococcus kloosii

    Article • Genome Announcements, May 2018, ASM Journals

    Dr Jean-François Pombert

  15. Complete Genome Sequence of Staphylococcus lutrae ATCC 700373, a Potential Pathogen Isolated from Deceased Otters

    Article • Genome Announcements, June 2017, ASM Journals

    Dr Jean-François Pombert

  16. Complete Genome Sequences of Two Human Oral Microbiome Commensals: Streptococcus salivarius ATCC 25975 and S. salivarius ATCC 27945

    Article • Genome Announcements, June 2017, ASM Journals

    Dr Jean-François Pombert, Robert Butler

  17. Genetic Characterization of the Exceptionally High Heat Resistance of the Non-toxic Surrogate Clostridium sporogenes PA 3679

    Article • Frontiers in Microbiology, April 2017, Frontiers

    Dr Jean-François Pombert, Robert Butler

  18. Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes

    Article • DNA Research, February 2017, Oxford University Press (OUP)

    Dr Jean-François Pombert, Dr Jean-François Brugère

  19. Enhancement of Microbial Biodesulfurization via Genetic Engineering and Adaptive Evolution

    Article • PLOS One, January 2017, PLOS

    Dr Jean-François Pombert, Robert Butler

  20. The ‘other’ coral symbiont: Ostreobium diversity and distribution

    Article • The ISME Journal, July 2016, Nature

    Dr Jean-François Pombert

  21. Complete Genome Sequences of Two Interactive Moderate Thermophiles,Paenibacillus napthalenovorans32O-Y andPaenibacillussp. 32O-W

    Article • Genome Announcements, February 2016, ASM Journals

    Dr Jean-François Pombert, Robert Butler

  22. Moramonas marocensis gen. nov., sp. nov.: a jakobid flagellate isolated from desert soil with a bacteria-like, but bloated mitochondrial genome

    Article • Open Biology, February 2016, Royal Society Publishing

    Dr Jean-François Pombert

  23. Erratum: Auxenochlorella protothecoides and Prototheca wickerhamii plastid genome sequences give insight into the origins of non-photosynthetic algae

    Article • Scientific Reports, December 2015, Nature

    Dr Jean-François Pombert, Professor David R Smith

  24. Genetic Diversity of Clostridium sporogenes PA 3679 Isolates Obtained from Different Sources as Resolved by Pulsed-Field Gel Electrophoresis and High-Throughput Sequencing

    Article • Applied and Environmental Microbiology, October 2015, ASM Journals

    Dr Jean-François Pombert, Robert Butler

  25. The Prediction and Validation of Small CDSs Expand the Gene Repertoire of the Smallest Known Eukaryotic Genomes

    Article • PLOS One, September 2015, PLOS

    Dr Jean-François Pombert

  26. Auxenochlorella protothecoides and Prototheca wickerhamii plastid genome sequences give insight into the origins of non-photosynthetic algae

    Article • Scientific Reports, September 2015, Nature

    Dr Jean-François Pombert, Professor David R Smith

  27. Isolation and characterization of an interactive culture of two Paenibacillus species with moderately thermophilic desulfurization ability

    Article • Biotechnology Letters, July 2015, Springer Science + Business Media

    Dr Jean-François Pombert, Robert Butler

  28. Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes

    Article • PLOS One, June 2015, PLOS

    Dr Jean-François Pombert, Robert Butler

  29. The Ordospora colligata Genome: Evolution of Extreme Reduction in Microsporidia and Host-To-Parasite Horizontal Gene Transfer

    Article • mBio, January 2015, ASM Journals

    Dr Jean-François Pombert, Mr. Shadi Beidas

  30. Helicosporidia: a genomic snapshot of an early transition to parasitism

    Article • Acta Societatis Botanicorum Poloniae, December 2014, Polish Botanical Society

    Dr Jean-François Pombert

  31. Evolution of a morphological novelty occurred before genome compaction in a lineage of extreme parasites

    Article • Proceedings of the National Academy of Sciences, October 2014, Proceedings of the National Academy of Sciences

    Dr Jean-François Pombert

  32. Exploiting the architecture and the features of the microsporidian genomes to investigate diversity and impact of these parasites on ecosystems

    Article • Heredity, September 2014, Nature

    Dr Jean-François Pombert, Robert Butler

  33. A Lack of Parasitic Reduction in the Obligate Parasitic Green Alga Helicosporidium

    Article • PLoS Genetics, May 2014, PLOS

    Dr Jean-François Pombert

  34. The Mitochondrial Genome of the Prasinophyte Prasinoderma coloniale Reveals Two Trans-Spliced Group I Introns in the Large Subunit rRNA Gene

    Article • PLOS One, December 2013, PLOS

    Dr Jean-François Pombert

  35. The complete mitochondrial genome from an unidentified Phalansterium species.

    Article • Protist Genomics, January 2013, De Gruyter

    Dr Jean-François Pombert

  36. Complete Genome Sequences from Three Genetically Distinct Strains Reveal High Intraspecies Genetic Diversity in the Microsporidian Encephalitozoon cuniculi

    Article • Eukaryotic Cell, January 2013, ASM Journals

    Dr Jean-François Pombert, Professor David R Smith

  37. Evidence for Transitional Stages in the Evolution of Euglenid Group II Introns and Twintrons in the Monomorphina aenigmatica Plastid Genome

    Article • PLOS One, December 2012, PLOS

    Dr Jean-François Pombert

  38. A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education

    Article • GigaScience, September 2012, Springer Science + Business Media

    Dr Jean-François Pombert, Wilfried Guiblet

  39. Tertiary Endosymbiosis in Two Dinotoms Has Generated Little Change in the Mitochondrial Genomes of Their Dinoflagellate Hosts and Diatom Endosymbionts

    Article • PLOS One, August 2012, PLOS

    Dr Jean-François Pombert

  40. Gain and loss of multiple functionally related, horizontally transferred genes in the reduced genomes of two microsporidian parasites

    Article • Proceedings of the National Academy of Sciences, July 2012, Proceedings of the National Academy of Sciences

    Dr Jean-François Pombert

  41. The mitochondrial genome of the arbuscular mycorrhizal fungus Gigaspora margarita reveals two unsuspected trans‐splicing events of group I introns

    Article • New Phytologist, February 2012, Wiley

    Dr Nicolas Corradi, Dr Jean-François Pombert

  42. The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins

    Article • Proceedings of the Royal Society B Biological Sciences, February 2012, Royal Society Publishing

    Dr Jean-François Pombert

  43. Acquisition of an animal gene by microsporidian intracellular parasites

    Article • Current Biology, August 2011, Elsevier

    Dr Nicolas Corradi, Dr Jean-François Pombert

  44. Branching Network of Proteinaceous Filaments within the Parasitophorous Vacuole ofEncephalitozoon cuniculiandEncephalitozoon hellem

    Article • Infection and Immunity, January 2011, ASM Journals

    Dr Jean-François Pombert

  45. The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis

    Article • Nature Communications, September 2010, Springer Science + Business Media

    Dr Nicolas Corradi, Dr Jean-François Pombert

  46. The Complete Plastid Genomes of the Two ‘Dinotoms’ Durinskia baltica and Kryptoperidinium foliaceum

    Article • PLOS One, May 2010, PLOS

    Dr Jean-François Pombert

  47. The Mitochondrial Genome of the Entomoparasitic Green Alga Helicosporidium

    Article • PLOS One, January 2010, PLOS

    Dr Jean-François Pombert

  48. Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions

    Article • Genome Biology, January 2009, Springer Science + Business Media

    Dr Nicolas Corradi, Dr Jean-François Pombert

  49. Evolutionary relationships among salivarius streptococci as inferred from multilocus phylogenies based on 16S rRNA-encoding, recA, secA, and secY gene sequences

    Article • BMC Microbiology, January 2009, Springer Science + Business Media

    Dr Jean-François Pombert

  50. The Green Algal Ancestry of Land Plants as Revealed by the Chloroplast Genome

    Article • International Journal of Plant Sciences, June 2007, University of Chicago Press

    Dr Jean-François Pombert

  51. The complete mitochondrial DNA sequence of the green alga Oltmannsiellopsis viridis: evolutionary trends of the mitochondrial genome in the Ulvophyceae

    Article • Current Genetics, May 2006, Springer Science + Business Media

    Dr Jean-François Pombert

  52. Article • BMC Biology, January 2006, Springer Science + Business Media

    Dr Jean-François Pombert

  53. The Chloroplast Genome Sequence of the Green Alga Pseudendoclonium akinetum (Ulvophyceae) Reveals Unusual Structural Features and New Insights into the Branching Order of Chlorophyte Lineages

    Article • Molecular Biology and Evolution, May 2005, Oxford University Press (OUP)

    Dr Jean-François Pombert

  54. The Complete Mitochondrial DNA Sequence of the Green Alga Pseudendoclonium akinetum (Ulvophyceae) Highlights Distinctive Evolutionary Trends in the Chlorophyta and Suggests a Sister-Group Relationship Between the Ulvophyceae and Chlorophyceae

    Article • Molecular Biology and Evolution, January 2004, Oxford University Press (OUP)

    Dr Jean-François Pombert