More About The Marcel van den Brink Lab Minus iconIcon indicating subtraction, or that the element can be closed. Plus IconIcon indicating addition, or that the element can be opened. Arrow (down) icon.An arrow icon, usually indicating that the containing element can be opened and closed.

Antonio Gomes, PhD

Computational Biologist, Sr.

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  • Post-Doctoral, Columbia University, 2014-2016
  • PhD, Bioinformatics, Boston University, 2008-2013.
  • MSc, Biophysics, Universidade de Brasília, 2005-2007.
  • BSc, Biology, Universidade de Brasília, 2001-2004 Major in Mathematics

Microbial community and GVHD

The human body is populated by a diverse microbial community that plays critical role in human physiology and health. Understanding microbial ecology, their metabolic capabilities and how they interact with the host can provide alternative therapies to human disease. I am particularly interested in identifying individuals in the gut microbial community that may play key roles in graft versus host disease. Ultimately, patient recovery can be improved by rational intervention that facilitates the growth of health microorganisms and reduce the presence of harmful species.

I use and develop statistical and mathematical models to analyze large volume of 16S, metagenomics and metabolomics to look for relationships between microorganisms and human host that may eventually lead to precise treatment of patients. Gut microbial communities can be selective modified towards a healthier state via diet (pre-biotics), antibiotic therapy or introduction of healthy microorganisms (probiotics). In order to exploit full potential of therapy, I am also interested in using synthetic ecology techniques to engineer key species that may improve control of microbial communities and facilitate the selection of a healthy community state.

Immune reconstitution

I also investigate cellular mechanisms that leads to immune reconstitution, particularly after bone marrow transplant.

I investigate multiple layers of next generation sequencing data (binding, expression and metabolomics, including single cell sequencing) to identify key regulators and genes that facilitate or inhibit immune recovery, with particular focus on key factors that may cause decline and recovery of thymus function.


Gomes ALC*, Johns N*, Wang HH, Promiscuity of regulatory elements in microbial communities, submitted.

Johns N*, Gomes ALC*, Wang HH, Metagenomics mining of regulatory elements for engineering diverse bacterial species and communities, submitted.

Johns N, Blazejewski T, Gomes ALC, Wang HH, Principles for Designing Synthetic Microbial Communities, Cur. Op. in Microbiol., 2016

Gomes ALC and Wang HH, The role of DNA accessibility in transcription factor binding in bacteria, PLOS Comp. Biol., 2016, 12(4): e1004891.

Gomes ALC, Abeel T, Peterson M, Azizi E, Lyubtskaya A, Carvalho L, Galagan J, Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction, Genome Research, 2014, 24, 1686-1697.

Gomes ALC, Galagan J, Segrè D, Resource competition may lead to effective treatment of antibiotic resistant infections, PLOS ONE, 2013, 8(12), e80775.

Galagan JE, Minch K*, Peterson M*, Lyubetskaya A*, Azizi E*, Sweet L*, Gomes A*, Rustad T, Dolganov G, Glotova I et al. The Mycobacterium tuberculosis Regulatory Network and the Hypoxic Response, Nature, 2013, 499, 178-183.
*Equal contributor