Bio


Working full time with bioinformatics for more than 13 years, I have had the opportunity to work mostly on: variant calling, bioinformatics pipeline development and automation, gene expression analysis by RNA-Seq, prokaryotic genome assembly and annotation, angiogenesis and machine learning.

Before joining Stanford as a postdoctoral scholar, I worked almost 5 years on a big clinical laboratory in Brazil named Diagnósticos da América (DASA), being responsible for the establishment and leadership of the bioinformatics department. My team was responsible for the validation/operation of multiple strategic products based NGS data as well as the bioinformatics support on selected research projects.

I am highly interested in biological questions that can be addressed by DNA sequencing, especially ideas that may be applied to improve general public health.

Professional Education


  • Doctor of Philosophy, University of Sao Paulo (2017)
  • Master of Science, University of Sao Paulo (2012)
  • Bachelor of Science, University of Sao Paulo (2010)

Stanford Advisors


Current Research and Scholarly Interests


Absolutely passionate about bioinformatics and biological questions that can be addressed by DNA sequencing, especially ideas that may be applied to improve general public health.

All Publications


  • A transcriptome-based signature of pathological angiogenesis predicts breast cancer patient survival PLOS GENETICS Guarischi-Sousa, R., Monteiro, J. S., Alecrim, L. C., Michaloski, J. S., Cardeal, L. B., Ferreira, E. N., Carraro, D. M., Nunes, D. N., Dias-Neto, E., Reimand, J., Boutros, P. C., Setubal, J. C., Giordano, R. J. 2019; 15 (12): e1008482

    Abstract

    The specific genes and molecules that drive physiological angiogenesis differ from those involved in pathological angiogenesis, suggesting distinct mechanisms for these seemingly related processes. Unveiling genes and pathways preferentially associated with pathologic angiogenesis is key to understanding its mechanisms, thereby facilitating development of novel approaches to managing angiogenesis-dependent diseases. To better understand these different processes, we elucidated the transcriptome of the mouse retina in the well-accepted oxygen-induced retinopathy (OIR) model of pathological angiogenesis. We identified 153 genes changed between normal and OIR retinas, which represent a molecular signature relevant to other angiogenesis-dependent processes such as cancer. These genes robustly predict the survival of breast cancer patients, which was validated in an independent 1,000-patient test cohort (40% difference in 15-year survival; p = 2.56 x 10-21). These results suggest that the OIR model reveals key genes involved in pathological angiogenesis, and these may find important applications in stratifying tumors for treatment intensification or for angiogenesis-targeted therapies.

    View details for DOI 10.1371/journal.pgen.1008482

    View details for Web of Science ID 000512336600011

    View details for PubMedID 31846472

    View details for PubMedCentralID PMC6917213

  • Comparative Analysis of Ralstonia solanacearum Methylomes FRONTIERS IN PLANT SCIENCE Erill, I., Puigvert, M., Legrand, L., Guarischi-Sousa, R., Vandecasteele, C., Setubal, J. C., Genin, S., Guidot, A., Valls, M. 2017; 8: 504

    Abstract

    Ralstonia solanacearum is an important soil-borne plant pathogen with broad geographical distribution and the ability to cause wilt disease in many agriculturally important crops. Genome sequencing of multiple R. solanacearum strains has identified both unique and shared genetic traits influencing their evolution and ability to colonize plant hosts. Previous research has shown that DNA methylation can drive speciation and modulate virulence in bacteria, but the impact of epigenetic modifications on the diversification and pathogenesis of R. solanacearum is unknown. Sequencing of R. solanacearum strains GMI1000 and UY031 using Single Molecule Real-Time technology allowed us to perform a comparative analysis of R. solanacearum methylomes. Our analysis identified a novel methylation motif associated with a DNA methylase that is conserved in all complete Ralstonia spp. genomes and across the Burkholderiaceae, as well as a methylation motif associated to a phage-borne methylase unique to R. solanacearum UY031. Comparative analysis of the conserved methylation motif revealed that it is most prevalent in gene promoter regions, where it displays a high degree of conservation detectable through phylogenetic footprinting. Analysis of hyper- and hypo-methylated loci identified several genes involved in global and virulence regulatory functions whose expression may be modulated by DNA methylation. Analysis of genome-wide modification patterns identified a significant correlation between DNA modification and transposase genes in R. solanacearum UY031, driven by the presence of a high copy number of ISrso3 insertion sequences in this genome and pointing to a novel mechanism for regulation of transposition. These results set a firm foundation for experimental investigations into the role of DNA methylation in R. solanacearum evolution and its adaptation to different plants.

    View details for DOI 10.3389/fpls.2017.00504

    View details for Web of Science ID 000398996000001

    View details for PubMedID 28450872

    View details for PubMedCentralID PMC5390034

  • Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii FRONTIERS IN PLANT SCIENCE Puigvert, M., Guarischi-Sousa, R., Zuluaga, P., Coll, N. S., Macho, A. P., Setubal, J. C., Valls, M. 2017; 8: 370

    Abstract

    Bacterial wilt of potatoes-also called brown rot-is a devastating disease caused by the vascular pathogen Ralstonia solanacearum that leads to significant yield loss. As in other plant-pathogen interactions, the first contacts established between the bacterium and the plant largely condition the disease outcome. Here, we studied the transcriptome of R. solanacearum UY031 early after infection in two accessions of the wild potato Solanum commersonii showing contrasting resistance to bacterial wilt. Total RNAs obtained from asymptomatic infected roots were deep sequenced and for 4,609 out of the 4,778 annotated genes in strain UY031 were recovered. Only 2 genes were differentially-expressed between the resistant and the susceptible plant accessions, suggesting that the bacterial component plays a minor role in the establishment of disease. On the contrary, 422 genes were differentially expressed (DE) in planta compared to growth on a synthetic rich medium. Only 73 of these genes had been previously identified as DE in a transcriptome of R. solanacearum extracted from infected tomato xylem vessels. Virulence determinants such as the Type Three Secretion System (T3SS) and its effector proteins, motility structures, and reactive oxygen species (ROS) detoxifying enzymes were induced during infection of S. commersonii. On the contrary, metabolic activities were mostly repressed during early root colonization, with the notable exception of nitrogen metabolism, sulfate reduction and phosphate uptake. Several of the R. solanacearum genes identified as significantly up-regulated during infection had not been previously described as virulence factors. This is the first report describing the R. solanacearum transcriptome directly obtained from infected tissue and also the first to analyze bacterial gene expression in the roots, where plant infection takes place. We also demonstrate that the bacterial transcriptome in planta can be studied when pathogen numbers are low by sequencing transcripts from infected tissue avoiding prokaryotic RNA enrichment.

    View details for DOI 10.3389/fpls.2017.00370

    View details for Web of Science ID 000396760400001

    View details for PubMedID 28373879

    View details for PubMedCentralID PMC5357869

  • Complete genome sequence of the potato pathogen Ralstonia solanacearum UY031 STANDARDS IN GENOMIC SCIENCES Guarischi-Sousa, R., Puigvert, M., Coll, N. S., Siri, M., Pianzzola, M., Valls, M., Setubal, J. C. 2016; 11: 7

    Abstract

    Ralstonia solanacearum is the causative agent of bacterial wilt of potato. Ralstonia solanacearum strain UY031 belongs to the American phylotype IIB, sequevar 1, also classified as race 3 biovar 2. Here we report the completely sequenced genome of this strain, the first complete genome for phylotype IIB, sequevar 1, and the fourth for the R. solanacearum species complex. In addition to standard genome annotation, we have carried out a curated annotation of type III effector genes, an important pathogenicity-related class of genes for this organism. We identified 60 effector genes, and observed that this effector repertoire is distinct when compared to those from other phylotype IIB strains. Eleven of the effectors appear to be nonfunctional due to disruptive mutations. We also report a methylome analysis of this genome, the first for a R. solanacearum strain. This analysis helped us note the presence of a toxin gene within a region of probable phage origin, raising the hypothesis that this gene may play a role in this strain's virulence.

    View details for DOI 10.1186/s40793-016-0131-4

    View details for Web of Science ID 000368621300001

    View details for PubMedID 26779304

    View details for PubMedCentralID PMC4714475