Denis Jacob Machado
Home PageEmailLinkedInGoogle Scholar
Dr. Denis Jacob Machado is an assistant professor in bioinformatics at the University of North Carolina at Charlotte (UNC Charlotte), College of Computing and Informatics (CCI), Department of Bioinformatics and Genomics (BiG), starting on Aug. 15, 2022. He was one of the first hires of the Computational Intelligence to Predict Health and Environmental Risks (CIPHER) research center. He is also the first Latine faculty at UNC Charlotte’s BiG.
Dr. Jacob Machado leads the Phyloinformatics Lab. The lab uses computational intelligence and phylogenetics to create an evolutionary framework integrating multi-omics data to answer practical questions in One Health. In response to the continued increase in the risk of zoonoses, the phyloinformatics lab has two main lines of research. First, investigate new pathogens’ emergence, evolution, and spread, focusing on preventing and treating infectious diseases. Second, create computational and molecular solutions to make data from biorepositories more readily available to biomedical research.
Highlights
-
Peer-reviewed publications on topics including genomics, evolution, parasitology, regeneration, emerging infectious diseases, and genomic epidemiology.
-
3+ years of experience using machine learning (e.g., PyTorch, TensorFlow), predictive modeling, high-throughput data processing, and data mining algorithms to solve practical problems.
-
10+ years of experience in molecular biology, high-throughput sequencing (e.g., Illumina, PacBio, Hi-C, GWAS, and RNA-Seq), sequence assembly, and differential gene expression analyses.
-
Concepts used in my current and past projects include Python, Flask, R, Shiny, Tableau, SQL, Git, Jupyter, AlphaFold2, RoseTTAFold, HADDOCK, SQL, and AWS.
Experience
August 15, 2022–Current
Assistant Professor in Bioinformatics, University of North Carolina at Charlotte, Charlotte–NC, USA.
- Head of the Phyloinformatics Lab at the College of Computing in Informatics (CCI), Department of Bioinformatics and Genomics (BiG), Computational Intelligence to Predict Health and Environmental Risks (CIPHER) research center.
- Dr. Jacob Machado is Brazilian. He was BiG’s first Latine faculty.
2019–2022
Postdoctoral Researcher, University of North Carolina at Charlotte, Charlotte–NC, USA.
- I studied the origins, evolution, and zoonotic events of coronaviruses. I also employed big data analysis to categorize different variants of SARS-CoV-2 and applied deep learning techniques to produce highly accurate structure predictions of their proteins.
- I predict how structural changes in the receptor-binding domain of the spike protein of different variants of SARS-CoV-2 may reduce antibody interaction without completely evading existing neutralizing antibodies (and, therefore, current vaccines).
- I created the first programs for gene prediction and annotation of Orthocoronavirinae (including SARS-COV-2) and Flaviviridae (including Hepatites C, yellow fever, dengue, and Zika virus) and deployed the pipelines as web applications.
- Produced draft genomes of highly regenerative echinoderms such as brittle stars and sea cucumbers for comparative genomics and tissue regeneration research.
2018–2019
Research Collaborator, Universidade de São Paulo, São Paulo–SP, Brazil.
- I built and administered the first computer clusters at the Muzeum of Zoology of the University of São Paulo (MUZUSP), providing training and technology to bridge the gap between basic animal research and applied bioinformatics with potential biomedical significance.
- I participated in the planning, funding acquisition, and implementation of the first laboratory to sequence historical DNA (e.g., from degraded museum samples) at the Department of Zoology of the University of São Paulo (USP).
- I developed new genome skimming techniques to retrieve genomic data of non-model organisms when samples were small or degraded. I also created the necessary software to facilitate the analysis of organelle genomes, including new indices that check for the completeness of circular genomes or misalignments in other types of contigs and scaffolds.
Invited Lecturer, Universidade de São Paulo, São Paulo–SP, Brazil.
- I created and taught the first graduate-level courses in bioinformatics and computer programming for biologists at USP’s Graduate Program in Zoology, ranked first in animal research worldwide for several years.
2017
Invited Lecturer, Universidad del Magdalena, Santa Marta D.T.C.H., Colombia.
- I designed and taught the first course in bioinformatics at the University of Magdalena. Classes included practical and theoretical lessons on DNA extraction and isolation, high-throughput sequencing, sequence alignment, reference, and de novo genome assembly, and gene prediction and annotation.
- I also consulted to faculty members involved in animal research who needed web and dry lab solutions for next-generation sequence analyses.
Education
- Ph.D. (Bioinformatics): Universidade de São Paulo (USP), São Paulo–SP, Brazil, 2018 (click here for the dissertation; doi: 10.11606/T.95.2018.tde-20012023-095836)
- M.Sc. (Zoology): Universidade de São Paulo (USP), São Paulo–SP, Brazil, 2013
- B.Sc. (Biological Sciences/ Marine Biology): Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), São Vicente–SP, Brazil, 2009
Random links
- My first name is Denis and my last name is Jacob Machado. I don’t have a middle name. Click here for an YouTube video where you can hear my name. Alternatively, click here for audio only.