Karen
Research path
I have a bachelor degree in Biology from Brazil at Unila. There I researched the interaction of two bacteria, Gluconacetobacter diazotrophicus and Azospirillum brasiliensis, and a fungi, Trichoderma harzianum, with the Mate plant, Ilex paraguariensis, under the direction of Cristian A. Rojas and Cleto Peres.
I am currently doing my PhD in Quebec with Hugo Germain and Isabel Desgagne-Penix at UQTR on Transcriptomics and metabolomics of Arabidopsis in response to fungal virulence proteins. Although my PhD program is in Cellular and molecular biology, I did all the analyses of my transcriptomic data and currently on my metabolomic data and I have collaborated in other projects throughout my PhD doing de novo transcriptome assembly, annotation and differential exon usage.
In 2018, I did an internship at Peter Solomon’s lab with Megan McDonald, where I used MinIon to sequence the genome of several isolates of the fungus Bipolaris sorokiniana, basecalled the reads and assembled them and finally aligned the new genomes to a reference to study structural changes in the chromosomes.
I also developed a R package for selection of reference genes from transcriptomic data (DOI: https://doi.org/10.1186/s12864-019-6426-2), you can access it on Github too.
Skills
MS Office
R and Bioconductor - Institut National de la Recherche Agronomique (France - 2017)
- Transcriptomic analysis
- Obtaining read count files from aligment files
- Differential expression analysis
- GO and KEGG enrichment analysis
- Gene co-expression analysis
- Transcriptomic analysis
Markdown
Python - Compute Quebec (Canada - 2017)
Unix - Compute Quebec (Canada - 2017)
High Performance Computing - Westgrid Summer School (Canada - 2020)
| Language | Read | Write | Speak | Understand | Native |
|---|---|---|---|---|---|
| English | Fluent | Advanced | Fluent | Fluent | |
| French | Fluent | Intermediary | Advanced | Fluent | |
| Portuguese | Fluent | Fluent | Fluent | Fluent | Yes |
| Spanish | Fluent | Yes | Advanced | Fluent |
Publications
Papers
2020
dos Santos, K.C.G., Desgagne-Penix, I. & Germain, H. Custom selected reference genes outperform pre-defined reference genes in transcriptomic analysis. BMC Genomics 21, 35 (2020) DOI: 10.1186/s12864-019-6426-2
2019
Fradj, N., dos Santos, K.C.G., Montigny, N., Awwad, F., Boumghar, Y., Germain, H., Desgagne-Penix, I. 2019. RNA-Seq de Novo Assembly and Differential Transcriptome Analysis of Chaga (Inonotus obliquus) Cultured with Different Betulin Sources and the Regulation of Genes Involved in Terpenoid Biosynthesis. International Journal of Molecular Sciences 20(18), 4334. DOI: 10.3390/ijms20184334
Lorrain, C., Goncalves dos Santos, K.C., Germain, H., Hecker, A. and Duplessis, S. 2019. Advances in understanding obligate biotrophy in rust fungi. New Phytol, 222: 1190-1206. DOI: 10.1111/nph.15641
2018
dos Santos, K.C.G., McDonald, M. 2018. High molecular weight DNA extraction for long read sequencing v1. Protocols.io, DOI: 10.17504/protocols.io.uppevmn
Ahmed, M.B., Santos, K.C.G.d., Sanchez, I.B. et al. 2018. A rust fungal effector binds plant DNA and modulates transcription. Sci Rep 8, 14718, DOI: 10.1038/s41598-018-32825-0
2013
dos Santos, K.C.G.; Lopez, D.S.H. ; Perez, L.M.; Roberti, L.; Schmid, P.; Figueiredo, I.; Peres, C.K.; C.A. Rojas. 2013. Gluconacetobacter diazotrophicus enhances growth initial stages of Ilex paraguariensis development. II Conferencia Iberoamericana de Interacoes Beneficas Microorganismos-Planta-Ambiente (IBEMPA), p. 450-451 (Extended abstract).
Oral presentations
2020
dos Santos, K.C.G., Desgagne-Penix, I. & Germain, H. 2020. Impact of fungal virulence proteins in plants. Centre SEVE Web Conferences (June 16th 2020), Canada.
2017
dos Santos, K.C.G., Desgagne-Penix, I. & Germain, H. 2017. Transcriptomic and metabolomic analysis of the alteration of physiological processes in a collection of transgenic plants expressing fungal effectors. Centre SEVE, Orford, Canada.
2014
dos Santos, K.C.G.; Lopez, D.S.H. ; Perez, L.M.; Roberti, L.; Schmid, P.; Figueiredo, I.; Peres, C.K.; Rojas, C.A. 2014. Analise da interacao endofitica entre microorganismos beneficos e a erva-mate. III Research Initiation Meeting - Unila - Research in the XXI century: challenges and possibilities, Foz do Iguacu, Brazil.
2013
dos Santos, K.C.G.; Lopez, D.S.H. ; Perez, L.M.; Roberti, L.; Schmid, P.; Figueiredo, I.; Peres, C.K.; Rojas, C.A. 2013. Avaliacao da resposta da erva-mate a inoculacao com microorganismos potencialmente beneficos. II Research Initiation Meeting - Unila, Foz do Iguacu, Brazil.
Poster presentations
2020
dos Santos, K.C.G., Desgagne-Penix, I. & Germain, H. 2019. Etude des plantes exprimant des proteines de virulence de la rouille du peuplier. Contest of scientific Posters - UQTR, Trois-Rivieres, Canada.
2019
dos Santos, K.C.G., Desgagne-Penix, I. & Germain, H. 2019. Transcriptomics and metabolomics of Arabidopsis expressing effectors from the poplar rust. Reunion conjointe Centre SEVE et SPPQ, Bromont, Canada.
dos Santos, K.C.G., Desgagne-Penix, I. & Germain, H. (2019). Effectors from poplar rust modulate Arabidopsis transcriptome. IS-MPMI 2019, Glasgow, United Kingdom.
dos Santos, K.C.G., Desgagne-Penix, I. & Germain, H. 2019. Custom selected reference genes outperform pre-defined reference genes in transcriptomic analysis. Plant Canada 2019, Guelph, Canada.
dos Santos, K.C.G., Desgagne-Penix, I. & Germain, H. 2019. Facteurs de virulence fongique modulent le transcriptome d’Arabidopsis. Contest of scientific Posters - UQTR, Trois-Rivieres, Canada.
2018
dos Santos, K.C.G., Desgagne-Penix, I. & Germain, H. 2018. Analysis of transcriptomic alterations in a collection of transgenic plants expressing fungal effectors. Plant Biology 2018, Montreal, Canada.
dos Santos, K.C.G., Desgagne-Penix, I. & Germain, H. 2018. Analysis of transcriptomic alterations in a collection of transgenic plants expressing fungal effectors. Contest of scientific Posters - UQTR, Trois-Rivieres, Canada.
2017
dos Santos, K.C.G., Desgagne-Penix, I. & Germain, H. 2017. Transcriptomic and metabolomic analysis of the alteration of physiological processes in a collection of transgenic plants expressing fungal effectors. Contest of scientific posters - UQTR, Trois-Rivieres, Canada.
2014
dos Santos, K.C.G.; Lopez, D.S.H. ; Perez, L.M.; Roberti, L.; Schmid, P.; Figueiredo, I.; Peres, C.K.; Rojas, C.A. 2014. Growth promotion of Ilex paraguariensis mediated by Gluconacetobacter diazotrophicus and its relation to nitrogen metabolism. VI South American Congress of Yerba Mate and II International Symposium of Yerba Mate and Health, Montevideo, Uruguay.
dos Santos, K.C.G.; Lopez, D.S.H. ; Perez, L.M.; Roberti, L.; Schmid, P.; Figueiredo, I.; Peres, C.K.; C.A. Rojas. 2014. Analise da interacao endofitica entre microorganismos beneficos e a erva-mate. III Research Initiation Meeting - Unila - Research in the XXI century: challenges and possibilities, Foz do Iguacu, Brazil.
2013
dos Santos, K.C.G.; Lopez, D.S.H. ; Perez, L.M.; Roberti, L.; Schmid, P.; Figueiredo, I.; Peres, C.K.; Rojas, C.A. 2013. Evaluacion de la respuesta de la yerba-mate a la inoculacion con microorganismos potencialmente beneficos. IV National and International Congress of Agrobiotechnology, Intellectual Property and Public Policies, Posadas, Argentina.
dos Santos, K.C.G.; Lopez, D.S.H. ; Perez, L.M.; Roberti, L.; Schmid, P.; Figueiredo, I.; Peres, C.K.; Rojas, C.A. 2013. Avaliacao da resposta da erva-mate a inoculacao com microorganismos potencialmente beneficos. II Research Initiation Meeting - Unila, Foz do Iguacu, Brazil.