Diogo Veiga

Diogo Veiga

Computational biologist

UNICAMP/School of Medicine

Biography

Diogo Veiga is a group leader and associated researcher at UNICAMP/School of Medicine. His research focuses on applying cutting-edge single-cell genomics and computational methods to study human diseases.

He has a broad expertise in Computational Biology and analysis of next-generation sequencing, including single-cell technologies, WGS, Exome-seq, RNA-seq, ATAC-seq and PacBio long read SMRT-seq.

Full list of publications is available at ORCID or Google Scholar.

Interests
  • Single-Cell Genomics
  • Bioinformatics/Computational Biology
  • Machine Learning
Education
  • Postdoctoral Fellow, 2016

    Institute for Immunology and Cancer Research, University of Montreal

  • PhD in Biomedical Sciences, 2012

    The University of Texas MD Anderson Cancer Center

  • MSc in Computer Science, 2006

    Federal University of Pernambuco

  • BSc in Computer Science, 2004

    BSc in Computer Science (Honors)

Skills

Computational Biology

Single-cell and bulk genomics

Machine Learning

Data Science

R for Data Science

Bioconductor | R package development | Tidyverse

Experience

 
 
 
 
 
University of Campinas - UNICAMP
Associate Researcher
University of Campinas - UNICAMP
Jan 2021 – Present Campinas, SP, Brazil

Activities:

  • Lead an externally funded research program at the UNICAMP School of Medicine focused on applying cutting-edge single-cell technologies to study neurological disorders.
  • Assembly of single-cell atlases of the human brain in healthy and diseased conditions using the multiome single-cell technology (paired chromatin accessibility and gene expression in single cells).
  • Analysis of single-cell genomic datasets, such as scRNA-seq and scATAC-seq.
  • Development of machine Learning approaches to identify gene regulatory networks at cell-type resolution.
  • Mentoring of students and postdocs.
 
 
 
 
 
The Jackson Laboratory for Genomic Medicine
Computational Scientist
The Jackson Laboratory for Genomic Medicine
Jul 2016 – Nov 2020 Connecticut, USA

Activities:

  • Lead the development of novel analytical pipelines for long-read sequencing technologies geared towards discovering tumor-specific isoforms in breast cancer (Science Advances, 2022).
  • Analysis of genomic datasets, such as RNA-seq, ATAC-seq and isoform sequencing with Pacbio long-read (SMRT-seq).
  • Apply Machine Learning to identify tumor-specific isoforms and RNA-based neoantigens for cancer immunotherapy.
  • Mentoring of lab members including students and postdocs.
  • Teaching R, Bioconductor and Genomics to scientists at JAX.
 
 
 
 
 
Institute for Immunology and Cancer Research, University of Montreal
Research Associate (Bionformatics)
Institute for Immunology and Cancer Research, University of Montreal
Oct 2012 – Jun 2016 Canada

Activities:

  • Research on T-acute lymphoblastic leukemia (T-ALL), an aggressive childhood blood cancer.
  • Analysis of genomics data such as RNA-seq, Exome-seq and ChIP-seq.
  • Analysis of mass spectrometry data (proteomics).
  • Developed a methodology to identify active regulators from RNA-seq and ChIP-seq datasets, which lead to the discovery of a network of genes that initiate T cell leukemia.
  • Developed a Shiny app to study pathway regulation in ChIP-seq data.
 
 
 
 
 
University of Texas MD Anderson Cancer Center
Research Trainee/PhD
University of Texas MD Anderson Cancer Center
Aug 2007 – Jul 2012 TX, USA

Activities:

  • Developed methods to characterize the transcriptional and non-coding RNA networks in M. Tuberculosis (Mtb) during macrophage infection.
  • Participated in TB PANNET Consortium (EU/USA), an international effort that carried out a comprehensive identification of non-coding RNAs in Mtb using a combination of custom microarrays and RNA-seq.
  • Development of methods to identify targets and pathways regulated by cis-encoded and trans-encoded non-coding RNAs.
 
 
 
 
 
National Laboratory for Scientific Computing
Bioinformatics Analyst
National Laboratory for Scientific Computing
Mar 2006 – May 2007 Brazil

Activities:

  • Reconstruction of Transcriptional Networks in Escherichia coli.
  • Developed a neural network to predict motif structures in transcriptional networks.
  • Analysis of microarrays for gene expression.
 
 
 
 
 
Center for Informatics, Federal University of Pernambuco
Masters Research
Center for Informatics, Federal University of Pernambuco
Mar 2004 – Feb 2006 Brazil

Activities:

  • Application of Bayesian networks and partial correlation analysis for reconstruction of gene regulatory networks (protein-DNA interactions) in yeast
  • Analysis of microarrays for gene expression.
 
 
 
 
 
Genomic Engineering Group, Federal University of Santa Catarina
Undergraduate Research
Genomic Engineering Group, Federal University of Santa Catarina
Jun 2002 – Feb 2004 Brazil

Activities:

  • Design and implementation of computational tools for modeling of metabolic and regulatory pathways using RDF graphs.
  • Design and implementation of object-oriented XML databases for genomic data.
 
 
 
 
 
Mathematics Department, Federal University of Santa Catarina
Teaching assistant
Mathematics Department, Federal University of Santa Catarina
Aug 2000 – Dec 2000 Brazil

Activities:

  • Linear Algebra and Analytical Geometry.