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. 2019 Dec 11. pii: evz270. [Epub ahead of print]. PMID: 31825473. 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 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. 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 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 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


Pombert Lab @ Illinois Tech

LS 340 Lifesciences building

3105 S Dearborn St

Chicago, IL 60616, USA

Office: +1 (312) 567-5745

Lab: +1 (312) 567-3414

Fax: +1 (312) 567-3494