Education

Ph.D. in Bioinformatics, University of São Paulo, 2015
M.Sc. in Computer Science, University of São Paulo
B.Sc. in Computer Science, Federal University of Ceará

Current Position

Postdoc at UCSF

Research Area

Copy number variation detection from whole-genome, whole-exome sequencing data

Simulation of SNPs, indels and structural variants

Protein-protein interaction networks

Data integration

 

Research Summary

PennCNV-Seq

Copy number variation detection from whole-genome, whole-exome sequencing data.

 

SVGen

Simulation of structural variants with precise breakpoints in next-generation sequencing data using short and long reads.

 

Publications

  1. de Araújo Lima et al., 2016. An integrative approach to investigate the respective roles of single-nucleotide variants and copy-number variants in Attention-Deficit/Hyperactivity Disorder (Nature Scientific Reports)
  2. Cappi et al., 2016. Whole-exome sequencing in obsessive-compulsive disorder identifies rare mutations in immunological and neurodevelopmental pathways (Nature Translational Psychiatry)
  3. Bastos et al., 2016. A Set of MiRNAs, Their Gene and Protein Targets and Stromal Genes Distinguish Early from Late Onset ER Positive Breast Cancer. (PLoS One)
  4. Salameh et al. 2015. PRUNE2 is a human prostate cancer suppressor regulated by the intronic long noncoding RNA PCA3 (PNAS)
  5. Maschietto et al. 2015. Co-expression network of neural-differentiation genes shows specific pattern in schizophrenia (BMC Medical Genomics)
  6. Coutinho-Camillo et al. 2015. Expression of apoptosis-regulating miRNAs and target mRNAs in oral squamous cell carcinoma (Cancer Genetics)
  7. Baumont et al., 2014. Innate immune response is differentially dysregulated between bipolar disease and schizophrenia (Schizophrenia research)
  8. Lima and Simões et al., 2014. Network-based disease gene prioritization by hitting time analysis (IEEE 14th International Conference on BioInformatics and BioEngineering)
  9. DelValle et al., 2014. Transcriptional profile of fibroblasts obtained from the primary site, lymph node and bone marrow of breast cancer patients (Genetics and molecular biology)
  10. Pintar et al., 2014. Early Gene Expression Changes in Skeletal Muscle from SOD1G93A Amyotrophic Lateral Sclerosis Animal Model (Cellular and molecular neurobiology)
  11. Maia et al., 2013. microRNA portraits in human vulvar carcinoma (Cancer Prevention Research)
  12. Grosso et al., 2013. Breast cancer tissue slices as a model for evaluation of response to rapamycin (Cell and tissue research)
  13. Silva et al., 2012. Transcriptional Alterations Related to Neuropathology and Clinical Manifestation of Alzheimer's Disease (PLoS ONE)
  14. Lima et al., 2012. Computing a Predictor Set Influence Zone through a Multi-Layer Genetic Network to Explore the Role of Estrogen in Breast Cancer (Advances in Breast Cancer Research)
  15. Campos et al., 2012. Differences in transcriptional effects of 1α,25 dihydroxyvitamin D3 on fibroblasts associated to breast carcinomas and from paired normal breast tissues (The Journal of Steroid Biochemistry and Molecular Biology)
  16. Maschietto et al., 2012. Gene expression of peripheral blood lymphocytes may discriminate patients with schizophrenia from controls (Psychiatry Research)
  17. Trapé et al., 2012. Gene Expression Profile in Response to Doxorubicin-Rapamycin Combined Treatment of HER-2-Overexpressing Human Mammary Epithelial Cell Lines (Molecular Cancer Therapeutics)
  18. Bando et al., 2011. Hippocampal CA3 transcriptome signature correlates with initial precipitating injury in refractory mesial temporal lobe epilepsy (PLoS ONE)
  19. Lima et al., 2011. Decreased AIRE Expression and Global Thymic Hypofunction in Down Syndrome (The Journal of Immunology)