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Angst P, Pombert JF, Ebert D, Fields PD. Near chromosome-level genome assembly of the microsporidium Hamiltosporidium tvaerminnensis. G3: Genes|Genomes|Genetics. jkad185, DOI: 10.1093/g3journal/jkad185.

Mascarenhas Dos Santos AC, Julian AT, Liang P, Juárez O,  Pombert JF. Telomere‑to‑Telomere genome assemblies
of human‑infecting Encephalitozoon species
BMC Genomics. 24:237. DOI: 10.1186/s12864-023-09331-3.


Mascarenhas Dos Santos AC, Julian AT, Pombert JF. The Rad9-Rad1-Hus1 DNA repair clamp is found in Microsporidia. Genome Biol Evol. 4(4):evac053. PMID: 35439302. DOI: 10.1093/gbe/evac053.

de Albuquerque NRM, Haag KL, Fields PD, Cabalzar A, Ben-Ami F, Pombert JF, Ebert D. A new microsporidian parasite, Ordospora pajunii sp. nov (Ordosporidae), of Daphnia longispina highlights the value of genomic data for delineating species boundaries. J Eukaryot Microbiol. 00:e12902. PMID: 35279911. DOI: 10.1111/jeu.12902.

Caesar L, Lopes AMC, Radaeski JN, Bauermann SG, Konzen ER, Pombert JF, Sattler A, Blochtein B,Carvalho AT, Haag KL. Longitudinal survey reveals delayed effects of low gene expression on stingless bee colony health. Journal of Apicultural Research. 61(5):654-663. DOI 10.1080/00218839.2021.1962123


Julian AT, Mascarenhas dos Santos AC, Pombert JF. 3DFI: a pipeline to infer protein function using structural homology. Bioinformatics Advances. 1(1):vbab030. DOI: 10.1093/bioadv/vbab030


Haag KL, Pombert JF, Sun Y, de Albuquerque NRM, Batliner B, Fields P, Lopes TF, Ebert D. Microsporidia with vertical transmission were likely shaped by nonadaptive processes. Genome Biol Evol. 2020. 12(1):3599-3614. PMID: 31825473. PMCID: PMC6944219. DOI: 10.1093/gbe/evz270


Lemieux C, Turmel M, Otis C, Pombert JF. A streamlined and predominantly diploid genome in the tiny marine green alga Chloropicon primus. Nature Communications. 2019. 10(1):4061. PMID: 31492891. PMCID: PMC6731263. DOI: 10.1038/s41467-019-12014-x

Hingston PA, Truelstrup Hansen L, Pombert JF, Wang S. Characterization of Listeria monocytogenes enhanced cold-tolerance variants isolated during prolonged cold storage. Int J Food Microbiol. 2019. 306:108262. PMID: 31362162. DOI: 10.1016/j.ijfoodmicro.2019.108262.

Sun Y, Veseli IA, Vaillancourt K, Frenette M, Grenier D, Pombert JF. 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. PLoS ONE. 2019. 14(4): e0216002. PMID: 31039174. PMCID: PMC6490898. DOI: 10.1371/journal.pone.0216002


Veseli IA, Mascarenhas dos Santos AC, Juárez O, Stark BC, Pombert JF. Complete genome sequence of Vitreoscilla sp. strain C1, source of the first bacterial hemoglobin. Microbiol Resour Announc. 2018. 7:e00922-18. PMID: 30533886. PMCID: PMC6256453. DOI: 10.1128/MRA.00922-18

Game Changer – Next Generation Sequencing and its Impact on Food Microbiology. Ronholm, J., Bidawid, S., Torriani, S., eds. (2018). Lausanne: Frontiers Media. DOI: 10.3389/978-2-88945-463-1 ISBN: 978-2-88945-463-1 ISSN: 1664-8714

Mascarenhas dos Santos AC, Jie R, Antunes Godoy H, Alves M, Pombert JF. Complete genomes of the potential zoonotic pathogens Staphylococcus felis and Staphylococcus kloosii. Genome Announc. 2018. 6(20):e00404-18. PMID: 29773625. PMCID: PMC5958265. DOI: 10.1128/genomeA.00404-18.


Veseli IA, Tang C, Pombert JF. Complete genome of Staphylococcus lutrae ATCC 700373, a potential pathogen isolated from deceased otters. Genome Announc. 2017. 5(25):e00572-17. PMID: 28642379. PMCID: PMC5481585. DOI: 10.1128/genomeA.00572-17 


Butler RR 3rd, Soomer-James J, Frenette M, Pombert JF. Complete genome sequences of two human oral microbiome commensals: Streptococcus salivarius ATCC 25975 and Streptococcus salivarius ATCC 27945. Genome Announc. 2017. 5(24):e00536-17. PMID: 28619805. PMCID: PMC5473274. DOI: 10.1128/genomeA.00536-17


Butler RR 3rd, Schill KM, Wang Y, Pombert JF. Genetic characterization of the exceptionally high heat resistance of the non-toxic surrogate Clostridium sporogenes PA 3679. Front. Microbiol. 2017. 8:545. PMID: 28421047. PMCID: PMC5376575. DOI: 10.3389/fmicb.2017.00545 


Belkorchia A, Pombert JF, Polonais V, Parisot N, Delbac F, Brugère JF, Peyret P, Gaspin C, Peyretaillade E. Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes. DNA Research. 2017. 24(3):251-260. PMID: 28338834. PMCID: PMC5499648. DOI: 10.1093/dnares/dsx002

Wang J, Butler RR 3rd, Wu F, Pombert JF, Kilbane JJ 2nd, Stark BC. Enhancement of microbial biodesulfurization via genetic engineering and adaptive evolution. PLoS ONE. 2017. 12(1):e0168833. PMID: 28060828. PMCID: PMC5218467. DOI: 10.1371/journal.pone.0168833

del Campo, J, Pombert JF, Šlapeta J, Larkum A, Keeling PJ. The ‘other’ coral symbiont: Ostreobium diversity and distribution. ISME J. 2017. 11(1):296-299. PMID: 27420029. PMCID: PMC5315466. DOI: 10.1038/ismej.2016.101


Strassert JFH, Tikhonenkov DV, Pombert JF, Kolisko M, Tai V, Mylnikov AP and Keeling PJ. Moramonas marocensis gen. nov., sp. nov.: a jakobid flagellate isolated from desert soil with a bacteria-like, but bloated mitochondrial genome. Open Biol. 2016. 6:150239. PMID: 26887409. PMCID: PMC4772810. DOI: 10.1098/rsob.150239


Butler RR 3rd, Wang J, Stark BC, and Pombert JF. Complete genome sequences of two interactive moderate thermophiles: Paenibacillus napthalenovorans 32O-Y and Paenibacillus sp. 32O-W. Genome Announc. 2016. 4(1):e01717-15. PMID: 26868401. PMCID: PMC4751325. DOI: 10.1128/genomeA.01717-15


Schill KM, Wang Y, Butler RR 3rd, Pombert JF, Reddy N, Skinner GE, and Larkin JW. Genetic diversity of Clostridium sporogenes PA3679 isolates obtained from different sources using pulsed-field gel electrophoresis (PFGE) and high-throughput sequencing. Appl Environ Microbiol. 2016. 82(1):384-393. PMID: 26519392. PMCID: PMC4702626. DOI: 10.1128/AEM.02616-15



Belkorchia A, Gasc C, Polonais V, Parisot N, Gallois N, Ribière C, Lerat E, Gaspin C, Pombert JF, Peyret P and Peyretaillade E. The prediction and validation of small CDSs expand the gene repertoire of the smallest known eukaryotic genomes. PLoS ONE. 2015. 10(9):e0139075. PMID: 26421846. PMCID: PMC4589312. DOI: 10.1371/journal.pone.0139075


Wang J, Davaadelgar B, Salazar JK, Butler RR 3rd, Pombert JF, John J. Kilbane JJ and Stark BC. Isolation and characterization of an interactive culture of two Paenibacillus species with moderately thermophilic desulfurization ability. Biotechnol Lett. 2015. 37(11):2201-2211. PMID: 26209032. DOI: 10.1007/s10529-015-1918-x


Yan D, Wang Y, Murakami T, Shen Y, Gong J, Jiang H, Smith DR, Pombert JF, Dai J and Wu Q. Auxenochlorella protothecoides and Prototheca wickerhamii plastid genome sequences give insight into the origins of non-photosynthetic algae. Sci Rep. 2015. 5:14465. PMID: 26403826. PMCID: PMC4585924. DOI: 10.1038/srep14465


Xiang H, Zhang R, Butler RR 3rd, Liu T, Zhang L, Pombert JF and Zeyang Zhou Z. Comparative analysis of codon usage bias patterns in microsporidian genomes. PLoS ONE. 2015. 10(6):e0129223. PMID: 26057384. PMCID: PMC4461291. DOI: 10.1371/journal.pone.0129223


Peyretaillade E, Boucher D, Parisot N, Gasc C, Butler RR 3rd, Pombert JF, Lerat E and Peyret P. Exploiting the architecture and the features of the microsporidian genomes to investigate diversity and impact of these parasites on ecosystems. Heredity. 2015. 114(5):441-449. PMID: 25182222. PMCID: PMC4815508. DOI: 10.1038/hdy.2014.78


Pombert JF, Haag KL, Beidas S, Ebert D and Keeling PJ. The Ordospora colligata genome; evolution of extreme reduction in microsporidia and host-to-parasite horizontal gene transfer. mBio. 2015. 6(1):e02400-14. PMID: 25587016. PMCID: PMC4313915. DOI: 10.1128/mBio.02400-14



Sun Y and Pombert JF. Helicosporidia: A genomic snapshot of an early transition to parasitism. Acta Soc Bot Pol. 2014. 83(4):377–385. DOI: 10.5586/asbp.2014.039


Pombert JF, Blouin NA, Lane C, Boucias D and Keeling PJ. A lack of parasitic reduction in the obligate parasitic green alga Helicosporidium. PLoS Genet. 2014. 10(5): e1004355. PMID: 24809511. PMCID: PMC4014436. DOI: 10.1371/journal.pgen.1004355


Haag KL, James TY, Pombert JF, Larsson R, Schaer TMM, Refardt D and Ebert D. Evolution of a morphological novelty occurred before genome compaction in a lineage of extreme parasites. Proc Natl Acad Sci USA. 2014. 111(43): 15480-15485. PMID: 25313038. PMCID: PMC4217409. DOI: 10.1073/pnas.1410442111



Pombert JF, Otis C, Turmel M and Lemieux C. The mitochondrial genome of the prasinophyte Prasinoderma coloniale reveals two trans-spliced group I introns in the large subunit rRNA gene. PLoS ONE. 2013. 8(12): e84325. PMID: 24386369. PMCID: PMC3873408. DOI: 10.1371/journal.pone.0084325


Pombert JF, Smirnov A, James ER, Janouškovec J, Gray MW and Keeling PJ. The complete mitochondrial genome from an unidentified Phalansterium species. Protist Genomics. 2013. 1: 25–32. DOI: 10.2478/prge-2013-0002


Pombert JF, Xu J, Smith DR, Heiman D, Young S, Cuomo CA, Weiss LM and Keeling PJ. Complete genome sequences from three genetically distinct strains reveal a high intra-species genetic diversity in the microsporidian Encephalitozoon cuniculi. Eukaryotic Cell. 2013. 12(4): 503-511. PMID: 23291622. PMCID: PMC3623445. DOI: 10.1128/EC.00312-12



Pombert JF‡, Selman M‡, Burki F, Bardell FT, Farinelli L, Solter LF, Whitman DW, Weiss LM, Corradi N and Keeling PJ. Gain and loss of multiple functionally related, horizontally transferred genes in the reduced genomes of two microsporidian parasites. Proc Natl Acad Sci USA. 2012. 109(31): 12638-12643. PMID: 22802648. PMCID: PMC3412028. DOI: 10.1073/pnas.1205020109 ‡equal contribution


Pombert JF, James ER, Janouškovec J and Keeling PJ. Evidence for transitional stages in the evolution of euglenid group II and group III introns and twintrons in the Monomorphina aenigmatica plastid genome. PLoS ONE. 2012. 5(1): e8954. PMID: 23300929. PMCID: PMC3534033. DOI: 10.1371/journal.pone.0053433


Pelin A‡, Pombert JF‡, Salvioli A, Bonen L, Bonfante P and Corradi N. The mitochondrial genome of the arbuscular mycorrhizal fungus Gigaspora margarita reveals two unsuspected trans-splicing events of group I introns. New Phytologist. 2012. 194:836-845. PMID: 22320438. DOI: 10.1111/j.1469-8137.2012.04072.x ‡equal contribution


Imanian B, Pombert JF, Dorrell RG and Keeling PJ. Tertiary endosymbiosis in two dinotoms has generated little change in the mitochondrial genomes of their dinoflagellate hosts and diatom endosymbionts. PLoS ONE. 2012. 7(8): e43763. PMID: 22916303. PMCID: PMC3423374. DOI: 10.1371/journal.pone.0043763


Oleksyk TK, Pombert JF, Siu D, Mazo-Vargas A, Ramos B, Guiblet W, Afanador Y, Ruiz-Rodriguez CT, Nickerson ML, Dean M, Logue D, Figueroa L, Valentin R and Martinez-Cruzado JC. A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education. GigaScience. 2012. 1:14. PMID: 23587420. PMCID: PMC3626513. DOI: 10.1186/2047-217X-1-14


Burki F, Okamoto N, Pombert JF and Keeling PJ. The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins. Proc. R. Soc. B. 2012. 279: 2246-2254. PMID: 22298847. PMCID: PMC3321700. DOI: 10.1098/rspb.2011.2301



Selman M, Pombert JF, Solter L, Farinelli L, Weiss LM, Keeling PJ and Corradi N. Acquisition of an animal gene by microsporidian intracellular parasites. Current Biology. 2011. 21(15): R576-577. PMID: 21820617. PMCID: PMC3751409. DOI: 10.1016/j.cub.2011.06.017

Oleksyk TK, Pombert JF, Guiblet W, Ramos B, Mazo A, Ruiz-Rodriguez CT, Nickerson ML, Winkler CA, Siu D, Valentin R, Figueroa L, Dean M, Logue D and Martinez-Cruzado JC. A Draft sequence of the Puerto Rican parrot genome (Amazona vittata) - a genome project funded by a local community effort. Nature Precedings. 2011. npre.2011.6552.1. (Not peer-reviewed). DOI: 10.1038/npre.2011.6552.1


Ghosh K, Nieves E, Keeling PJ, Pombert JF, Henrich PP, Cali A and Weiss LM. A branching network of proteinaceous filaments within the parasitophorous vacuole of Encephalitozoon cuniculi and Encephalitozoon hellem. Infection and Immunity. 2011. 79(3):1374-1385. PMID: 21220485. PMCID: PMC3067493. DOI: 10.1128/IAI.01152-10



Pombert JF and Keeling PJ. The mitochondrial genome of the entomoparasitic green alga Helicosporidium. PLoS ONE. 2010. 5(1): e8954. PMID: 20126458. PMCID: PMC2813288. DOI: 10.1371/journal.pone.0008954


Corradi C‡, Pombert JF‡, Farinelli L, Didier ES and Keeling PJ. The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis. Nature Communications. 2010. 1:77. PMID: 20865802. PMCID: PMC4355639. DOI: 10.1038/ncomms1082 ‡equal contribution


Imanian B‡, Pombert JF‡ and Keeling PJ. The complete plastid genomes of the two 'dinotoms' Durinskia baltica and Kryptoperidinium foliaceum. PLoS ONE. 2010. 5(5): e10711. PMID: 20502706. PMCID: PMC2873285. DOI: 10.1371/journal.pone.0010711 ‡equal contribution


2009 and earlier

Pombert JF, Sistek V, Boissinot M and Frenette M. Evolutionary relationships among salivarius streptococci as inferred from multilocus phylogenies based on 16S rRNA-encoding, recA, secA, and secY gene sequences. BMC Microbiology. 2009. 9:232. PMID: 19878555. PMCID: PMC2777182. DOI: 10.1186/1471-2180-9-232


Corradi C, Haag KL, Pombert JF, Ebert D and Keeling PJ. 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. Genome Biology. 2009. 10:R106. PMID: 19807911. PMCID: PMC2784321. DOI: 10.1186/gb-2009-10-10-r106


Turmel M, Pombert JF, Charlebois P, Otis C and Lemieux C. The green algal ancestry of land plants as revealed by the chloroplast genome. International Journal of Plant Sciences. 2007. 168:679–689. DOI: 10.1086/513470


Pombert JF, Beauchamp P, Otis C, Lemieux C and Turmel M. The complete mitochondrial DNA sequence of the green alga Oltmannsiellopsis viridis: Evolutionary trends of the mitochondrial genome in the Ulvophyceae. Current Genetics. 2006. 50:137-147. PMID: 16721603. DOI: 10.1007/s00294-006-0076-z


Pombert JF, Lemieux C and Turmel M. The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes. BMC Biology. 2006. 4:3. PMID: 16472375. PMCID: PMC1402334. DOI: 10.1186/1741-7007-4-3


Pombert JF, Otis C, Lemieux C and Turmel M. 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. Molecular Biology and Evolution. 2005. 22:1903-1918. PMID: 15930151. DOI: 10.1093/molbev/msi182


Pombert JF, Otis C, Lemieux C and Turmel M. 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. Molecular Biology and Evolution. 2004. 21:922-935. PMID: 15014170. DOI: 10.1093/molbev/msh099


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