(PDF files are available on request. Send a mail to gertraud.burger{at}umontreal.ca)
"Eukan: a fully automated nuclear genome annotation pipeline for less studied and divergent eukaryotes." Bioinformatics, submitted, Manuscript ID BIOINF-2025-0527
"Microbes beneficial to cranberry plants." ISHS Acta Horticulturae ##, XIII Vaccinium Symposium (Percival D, Polashock J, Retamales J, eds)   doi: ##
"A draft genome sequence of Diaporthe vaccinii, isolated from diseased cranberries." Microbiol Resour Announc, revision with the editor, manuscript nr. MRA00466-24R1
"A biofertilizing fungal endophyte of cranberry plants suppresses the plant pathogen Diaporthe." Front Microbiol 15:1327392   doi: fmicb.2024.1327392     Abstract
"Subunit composition of mitochondrial dehydrogenase complexes in diplonemid flagellates." BBA - General Subjects 1867(9):130419   doi: 10.1016/j.bbagen.2023.130419     Abstract
"Mitochondrial genome annotation with MFannot: a critical analysis of gene identification and gene model prediction." Frontiers Plant Sci 14:12222186   doi: 10.3389/fpls.2023.1222186     Abstract
"Miniature RNAs are embedded in an exceptionally protein-rich mitoribosome via an elaborate assembly pathway." Nucleic Acid Res 51(12):6443-6460   doi: 10.1093/nar/gkad422     Abstract
"Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes." BMC Biol 21:99   doi: 10.1186/s12915-023-01563-9     Abstract
"Nuclear genome sequence and gene expression of an intracellular fungal endophyte stimulating the growth of cranberry plants." J Fungi 9(1):126   doi:10.3390/jof9010126     Abstract
"Endosymbionts in cranberries: diversity and effect on plant growth and pathogen biocontrol." Plant People Planet 1:1-12   doi:10.1002/ppp3.10290
"Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs." Molec Phylo Evol 159:107088   doi:10.1016/j.ympev.2021.107088     Abstract
"Unexpectedly complex mitoribosomes in Andalucia godoyi, a protist with the most bacteria-like mitochondrial genome." Molec Biol Evol 38(3):788-804   doi:10.1093/molbev/msaa223     Abstract
"Targeted integration by homologous recombination enables in-situ tagging and replacement of genes in the marine microeukaryote Diplonema papillatum." Environ Microbiol 22(9):3660-3670   doi:10.1111/1462-2920.15130     Abstract
"Genetic tool development in marine protists: Emerging model organisms for experimental cell biology." Nature Methods   doi:10.1038/s41592-020-0796-x     Abstract   Science Web   Springer Nature Blog   Moore Foundation Web   Editorial
"Gene fragmentation and RNA editing without borders: eccentric mitochondrial genomes of diplonemids." Nucleic Acids Res 48(5):2694-2708   doi:10.1093/nar/gkz1215     Abstract
"The draft genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome." BMC Biol 18(1):22   doi:10.1186/s12915-020-0741-6     Abstract
"An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins." eLife 8:e42535   doi:10.1101/462648     Abstract
"Respiratory chain Complex I of unparalleled divergence in diplonemids." J Biol Chem 293(41):16043-16056   doi:10.1074/jbc.RA118.005326     Abstract
"Perfection of eccentricity: mitochondrial genomes of diplonemids." IUBMB Life 70(12):1197-1206   doi:10.1002/iub.1927     Abstract
"Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPase." Sci Reports 8:5239   doi:10.1038/s41598-018-23575-0     Abstract
"Transformation of Diplonema papillatum, the type species of the highly diverse and abundant marine micro-eukaryotes Diplonemida (Euglenozoa)." Environ Micobiol 20:1030-1040   doi:10.1111/1462-2920.14041     Abstract
"Keeping it complicated: mitochondrial genome plasticity in diplonemids." Sci Reports 7:14166   doi:10.1038/s41598-017-14286-z   Abstract
"Post-transcriptional mending of gene sequences: looking under the hood of mitochondrial gene expression in diplonemids." RNA Biol 13(12):1204-1211   Abstract
"Genes in hiding." Trends Genet 32(9):535-565   doi:10.1016/j.tig.2016.06.005   Abstract
"Non-functional genes repaired at the RNA level." C R Biol 339:289-295   doi:10.1016/j.crvi.2016.04.004   Abstract, PDF
"Expansion of signal transduction pathways in fungi by whole-genome duplication." Current Biol 26(12):1577-1584   Abstract
"Novel modes of RNA editing in mitochondria." Nucleic Acids Res 44(10):4907-4919   doi:10.1093/nar/gkw188   Abstract
"Three-dimensional structure model and predicted rewiring of ATP interactions of a deviant RNA ligase." BMC Struct Biol 15:20-34   Abstract
"Programmed translational bypassing elements in mitochondria: structure, mobility and evolutionary origin." Trends Genet 31(4):197-194   Abstract
"Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules." Nucleic Acids Res 42:13764-13777   Abstract
"Massive programmed translational jumping in mitochondria." Proc Natl Acad Sci USA 111(16):5926-5931   Abstract
"Trans-splicing and RNA-editing of LSU rRNA in Diplonema mitochondria." Nucleic Acids Res 42:517-528   Abstract
"Earliest holozoan expansion of phosphotyrosine signaling." Molec Biol Evol 31:517-528   Abstract
"A second eukaryotic group with mitochondrion-encoded tmRNA. in silico identification and experimental confirmation." RNA Biology 10:1117-1124   Abstract
"A strikingly bacteria-like and gene-rich mitochondrial genome is a hallmark of jakobid protists." Genome Biol Evol 5:418-438   Abstract
"RNA-level unscrambling of fragmented genes in Diplonema mitochondria." RNA Biology 10:301-313   Abstract
"Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants." Science 335:843-847   Abstract
"Unscrambling genetic information at the RNA level." (invited review) Wiley Interdiscip Rev RNA 3:213-228   Abstract
"Gene fragmentation: a key to mitochondrial genome evolution in Euglenozoa?" Curr Genet 57(4):225-232   Abstract
"Evolutionary conserved trans-splicing without cis-motifs." Mol Biol Evol 28(9):2425-2428   Abstract
"Systematically fragmented genes in a multi-partite mitochondrial genome." Nucleic Acids Res 39(3):979-988   Abstract
"TESTLoc: protein subcellular localization prediction from EST data." BCM Bioinformatics 11:563   Abstract
"Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles." Molec Biol Evol 27(7):1698-1709   Abstract
"Abundant 5S rRNA-like transcripts encoded by the mitochondrial genome in amoebozoa." Eukaryotic Cell 9(5):762-773   Abstract
"Group I-intron trans-splicing and mRNA editing in the mitochondria of placozoan animals." Trends Genet 25(9):381-386   Abstract
"Diversity and dispersal of a ubiquitous protein family: acyl-CoA dehydrogenases." Nucleic Acids Res 37(17):5619-5631   Abstract
"Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication." PLoS Genetics 5(7):e1000459   Abstract
"Distribution and phylogeny of EFL and EF-1 in Euglenozoa suggest ancestral co-occurrence followed by differential loss." PLoS One 4(4):e5162   Abstract
"GOBASE: an organelle genome database." Nucleic Acids Res 37:D946-950   Abstract
"Plasticity of a key metabolic pathway in fungi." Funct Integrat Genomics 9:145-151   Abstract
"Unassigned MURF1 of kinetoplastids codes for NADH dehydrogenase subunit 2." BMC Genomics 9:455   Paper
"Function prediction of hypothetical proteins without sequence similarity to proteins of known function." Pept Lett 15(10):1107-1116   Abstract
"Evolution of C2H2-zinc finger genes and subfamilies in mammals: Species-specific duplication and loss of clusters, genes and effector domains." BMC Evol Biol 8:176   Abstract
"Methodology for constructing problem definitions in bioinformatics." Bioinformatics and Biology Insights 2:239-244   Abstract
"Quand les gènes s'éclatent: les génomes des diplonémidés (When genes break up: the mitochondrial genomes of diplonemids)." Médecine Science 24:703-705   Abstract
"A phylogenomic investigation into the origin of Metazoa." Mol Biol Evol 25:664-672   Abstract
"Mitochondrial DNA as a genomic jigsaw puzzle." Science 318:415   Abstract
"Unite and conquer: enhanced prediction of protein subcellular localization by integrating multiple specialized tools." BMC Bioinformatics 8:420-430   Abstract
"Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans." Current Biol 17:1420-1425   Abstract
"Unusual mitochondrial genome structures throughout Euglenozoa." Protist 158:385-396   Abstract
"Purification of mitochondrial and plastid DNA." Nat Protoc 2:652-660   Abstract
"Sequencing complete mitochondrial and plastid genomes." Nat Protoc 2:603-614   Abstract
"The origins of multicellularity: a multi-taxon genome initiative." Trends Genet 23:113-118   Abstract
"Mitochondrial introns - a critical view." Trends Genet 23:119-125   Abstract
"Rhynchopus euleeides n. sp. (Diplonemea), a free-living, marine euglenozoan." J Eukaryot Microbiol 54:137-145   Abstract
"TBestDB: a taxonomically broad database of expressed sequence tags (ESTs)." Nucleic Acids Res 35:D445-451   Abstract
"Dynamics of an 89-kDa protein localizing at a specialized tip of the endonuclear symbiotic bacterium Holospora in infection." Jpn J Protozool 39:89-90   Abstract
"Comparative Analysis of Gender-Associated, Complete Mitochondrial Genomes in Marine Mussels (Mytilus spp.)." Genetics 172:1107-1119   Abstract
"GOBASE - a database of organelle and bacterial genome information." Nucleic Acids Res 34:D697-699   Abstract
"Translocation of an 89-kDa periplasmic protein is associated with Holospora infection." Biochem Biophys Res Comm 337:1198-1205   Abstract
"On the origin of mitochondria and Rickettsia-related eukaryotic endosymbionts." Jpn J Protozool 38(2):171-183
"The Tree of Eukaryotes." Trends in Ecology & Evolution 20(12):670-676   Abstract
"The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region." Nucleic Acids Res 33(14):4433-4442   Abstract
"Monophyly of primary photosynthetic eukaryotes: green plants, red algae and glaucophytes." Curr Biol 15:1325-1330   Abstract
"AutoFACT: An Automatic Functional Annotation and Classification Tool." BMC Bioinformatics 6:151   Abstract
"Unique mitochondrial genome structure in diplonemids, the sister group of kinetoplastids." Eukaryot Cell 4(6):1137-1146   Abstract
"Mitochondria of protists." (invited review) Annu Rev Genet 38:477-524   Abstract
"FLOSYS - a web-accessible workflow system for protocol-driven biomolecular sequence analysis." Cell Mol Biol 50(7):785-793   Abstract
"AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis" BMC Bionformatics 4:63   Abstract
"Mitochondrial genomes, anything goes." (invited review) Trends in Genetics 19(12):709-716   Abstract
"Parallels in genome evolution in mitochondria and bacterial symbionts." (invited review) IUBMB Life 55(4-5):205-212   Abstract
"The enigmatic mitochondrial ORF ymf39 codes for ATP synthase chain b." Nucl Acids Res 31 (9):2353-2360   Abstract
"Phylogenetic relationship of non-mitochondrial nucleotide transport proteins in bacteria and eukaryotes." Gene 306:27-35   Abstract
"Unique mitochondrial genome architecture in unicellular relatives of animals." Proc Natl Acad USA 100:892-897   Abstract
"GOBASE: a database of mitochondrial and chloroplast information." Nucl Acids Res 1:176-178   Abstract
"Structure of the bc1 complex from Seculamonas ecuadoriensis, a jakobid flagellate with in ancestral mitochondrial genome." Mol Biol Evol 20:145-153   Abstract
"The closest unicellular relatives of animals." Current Biology 12:1773-1778   Abstract
"Building a genome database using an object-oriented approach." In: In silico Biology 2 (3):213-217   Abstract
"The origin and early evolution of mitochondria." (invited review) Genome Biology 2(6), reviews 1018.1-1018.5   Abstract
"GOBASE: the Organelle Genome Database." Nucl Acids Res 29(1):128-132   Abstract
"Early eukaryote evolution based on mitochondrial gene order breakpoints." J Comput Biol 7(3):521-535   Abstract
"A novel motif for identifying Rps3 homologs in fungal mitochondrial genomes." TIBS 25:363-365. No abstract available.
"The mitochondrial genome of the stramenopile alga Chrysodidymus synuroideus. Complete sequence, gene content and genome organization." Nucleic Acids Res 28:2512-2518   Abstract
"The complete mitochondrial DNA sequence of Scenedesmus obliquus reflects an intermediate stage in the evolution of the green algal mitochondrial genome." Genome Research 10:819-831   Abstract
"Complete sequence of the mitochondrial genome of Tetrahymena pyriformis and comparison with Paramecium aurelia mitochondrial DNA." J Mol Biol 297:365-380   Abstract
"Expression of mitochondrial protein-coding genes in Tetrahymena pyriformis." J Mol Biol 297:381-393   Abstract
"L'évolution moléculaire et la révolution génomique." (invited review) Medecine Science 16:212-218
"Early eukaryote evolution based on mitochondrial gene order breakpoints." Proceedings of the Fourth Annual International Conference on Computational Molecular Biology (RECOMB 2000), pp. 254-262. New York: ACM Press
"A mitochondrial marker for red algal intraspecific relationships. Variable within populations and maternally inherited in Bostrychia." Mol Ecology 8:1443-1447   Abstract
"Mitochondrial genome evolution and the origin of eukaryotes." (invited review) Annu Rev Genet 33:351-397   Abstract
"A comparative genomics approach to the evolution of eukaryotes and their mitochondria." (invited review) J Euk Microbiol 46:320-326   Abstract
"Complete sequences of the mitochondrial DNA of the red alga Porphyra purpurea: Cyanobacterial introns and shared ancestry of red and green algae." Plant Cell 11:1675-1694   Abstract
"The complete mitochondrial DNA sequences of Nephroselmis olivacea and Pedinomonas minor: Two radically different evolutionary patterns within green algae." Plant Cell 11:1717-1729   Abstract
"Mitochondrial evolution." (invited review) Science 283:1476-1481   Abstract
"Mitochondrial genomics in protists, an approach to probing eukaryotic evolution." (invited review) Protist 149:313-322
"The Organelle Genome Database Project (GOBASE)." Nucleic Acids Res 26:139-144   Abstract
"Genome Structure and gene content in protist mitochondrial DNAs." Nucleic Acids Res 26:865-887   Abstract
"An ancestral mitochondrial DNA resembling a eubacterial genome in miniature." Nature 387:493-497   Abstract
"Utility of the mitochondrial nad4L gene for algal and protistan phylogenetic analysis." J Phycol 32:452-456   Abstract
"Genes encoding the same three subunits of respiratory complex II are present in the mitochondrial DNA of two phylogenetically distant eukaryotes." Proc Natl Acad Sci USA 93:2328-2332   Abstract
"The mitochondrial DNA of the amoeboid protozoon, Acanthamoeba castellanii. Complete sequence, gene content and genome organization." J Mol Biol 245:522-537   Abstract
"Complete sequence of the mitochondrial DNA of the chlorophyte alga Prototheca wickerhamii. Gene content and genome organization." J Mol Biol 237:74-86   Abstract
"Extrachromosomal plasmids in the plant pathogenic fungus Rhizoctonia solani." Curr Genetics 25:423-431   Abstract
"Mitochondrial genes in the colorless alga Prototheca wickerhamii resemble plant genes in their exons but fungal genes in their introns." Nucleic Acids Res 21:719-726   Abstract
"nirA, the pathway-specific regulatory gene of nitrate assimilation in Aspergillus nidulans encodes a putative GAL4-type zinc-finger protein and contains 4 introns in highly conserved regions." Mol Cell Biol 11:5746-5755   Abstract
"Heterologous expression of the Aspergillus nidulans regulatory gene nirA in Fusarium oxysporum." Gene 109:155-160   Abstract
"Molecular cloning and functional characterization of the pathway specific regulatory gene nirA, controlling nitrate assimilation in Aspergillus nidulans." Mol Cell Biol 11:795-802   Abstract
"A rapid, high resolution DNA sequencing gel system." Anal Biochem 188:176–180 Abstract
"A collection of programs for nucleic acid and protein analysis, written in FORTRAN 77 for IBM-PC compatible microcomputers." Nucleic Acids Res 14:455–465 Abstract
"Mitochondrial gene URFN gene of Neurospora crassa codes for a long polypeptide with a highly repetitive structure." J Mol Biol 191:589–599 Abstract
"The mitochondrial URF1 gene in Neurospora crassa has a novel type of intronic URF." J Mol Biol 186:231–242 Abstract
"Processing in Neurospora crassa mitochondria: Transfer RNAs punctuate a large precursor transcript." EMBO J 4:197–204 Abstract
"Cytochrome b of cob revertants in yeast. 2. Bioenergetic characterization of revertants with reduced content and shifted maximum absorption wavelength of cytochrome b." Eur J Biochem 141:299–304 Abstract
"Cytochrome b of cob revertants in yeast. 1. Isolation and characterization of revertants derived from cob exon mutants of Saccharomyces cerevisiae." Mol Gen Genet 196:158–166 Abstract
"Subunit 1 of cytochrome oxidase from Neurospora crassa: Nucleotide sequence of the coding gene and partial amino acid sequence of the protein." EMBO J 1:1385–139 Abstract
"Extrachromosomal inheritance in Schizosaccharomyces pombe. III. Isolation and characterization of paromomycin-resistant mutants." Mol Gen Genet 152:319–324 Abstract
"A simple method for the large-scale preparation of mitochondria from microorganisms." Anal Biochem 77:110–121 Abstract
"Antimycin resistance in Saccharomyces cerevisiae: a new mutation on the mitDNA conferring antimycin resistance on the mitochondrial respiratory chain." Biochem Biophys Res Commun 72:1201–1208 Abstract
"Extrachromosomal inheritance in Schizosaccharomyces pombe. II. Evidence for extrakaryotically inherited respiratory deficient mutants." Mol Gen Genet 144:75–81 Abstract
"Extrachromosomal inheritance in Schizosaccharomyces pombe. I. Evidence for an extrakaryotically inherited mutation conferring resistance to antimycin." Mol Gen Genet 144:67–73 Abstract
"Studies on the mechanism of electron transport in the bc1-segment of the respiratory chain in yeast. III. Isolation and characterization of an antimycin resistant mutant ANT 8 in Schizosaccharomyces pombe." Mol Gen Genet 137:353–363 Abstract
"Studies on the mechanism of electron transport in the bc1-segment of the respiratory chain in yeast. II. The binding of antimycin to mitochondrial particles and the function of two different binding sites." Biochim Biophys Acta 396:187–201 Abstract
"Activity of reduced ubiquinone: cytochrome c oxidoreductase with various ubiquinol-isoprenologues as substrate and corresponding inhibitory effect of antimycin in yeast." Biochim Biophys Acta 368:71–85 Abstract