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L. Thibério Rangel, Ph.D.

Computational Biologist @Finch Therapeutics


Email:
Lattes
Google Scholar

My research is based on Evolutionary Genomics and Microbial Data Science to understand the association between gain/loss of genes and the colonization of new niches/environments. I am particularly interested in applying network analyzes to complex biological datasets.

Currently, I am a Computational Biologist at Finch Therapeutics's Data Science team working on human gut microbiome!

My research experience comprehend:
  • Evolutionary Genomics;
  • In-silico protein annotation;
  • Human Microbiome;
  • Molecular evolution;
  • Statistical analysis of biological data;
  • Statistical clustering;
Experience

Research Scientist II, Computational Biology

Institution: Finch Therapeutics, Somerville, MA, USA
Period: Jul 2021 - Present
Key workstreams:

  • Lead data analyst in a cross-functional team;
  • Microbiome community characterization and differential abundance;
  • Development of tools for automated protein annotation and pathway detection;

Postdoctoral Associate

Institution: Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
Supervisor: Greg Fournier
Period: Apr 2018 - Jun 2021
Key workstreams:

  • Non-phylogenetic identification of gene co-evolution networks;
  • Modeling of among site substitution rate heterogeneity;
  • Application of Horizontal Gene Transfers to expand time calibration constraints (bayesian molecular clocks);

Postdoctoral Fellow

Simons Foundation Fellow
Institution: Universidade de São Paulo (USP), São Paulo, São Paulo, Brazil
Supervisor: João Carlos Setubal
Period: Sep 2017 - Mar 2018

  • Application of Horizontal Gene Transfers to expand time calibration constraints (bayesian molecular clocks);

Education

Ph.D. in Bioinformatics

Institution: Universidade de São Paulo (USP), São Paulo, São Paulo, Brazil
Title: Phylogenetic Networks and Horizontal Gene Transfer.
Advisor: João Carlos Setubal
Period: Jul 2012 - Aug 2017
Visiting researcher: one year in Peter Gogarten's lab at University of Connecticut as part of my Ph.D. research (from 04/2015 to 03/2016)
Fellowship: FAPESP

M.Sc. in Host-Pathogen-Relationship Biology

Institution: Universidade de São Paulo (USP), São Paulo, São Paulo, Brazil
Title: Development of EGene platform for functional annotation and database integration: application and validation on transcript sequences of Eimeria spp. of domestic fowl.
Advisor: Arthur Gruber
Period: Sep 2009 - Jan 2012
Fellowship:FAPESP

B.Sc. in Biological Sciences

Institution: Universidade Federal da Paraíba (UFPB), João Pessoa, Paraíba, Brazil
Title: Development of an online tool, GIAnT, for genomic island prediction on bacteria.
Advisor: Demetrius Antônio Machado de Araujo
Period: Jul 2005 - Apr 2009
Fellowship:CNPq

Developed tools (a.k.a Portfolio)

Python package for assessing Evolutionary Similarity Indices between gene families
Description: Jupyter Notebook and Python package for assessing evolutionary similarities between gene families.

The Eimeria Transcript Database
Description: web interface to access transcript database. Allows the user to interact with transcripts through BLAST and/or keyword searches. Developed as part of masters thesis together with automatic protein annotation components (related publications listed bellow). Written in Perl(backend and frontend) and PHP (frontend).

GIAnT - Genomic Island Analyzer Tool
Description: web tool to predict genomic island through bias in genome content. Six different composition metrics implemented. Developed as part of undergraduate research. Written in Python (CherryPy).

Technical skills

Statistics: Strong knowledge of statiscal methods applied to bioinformatics.

Python: Advanced
well versed in several data analysis libraries (e.g. Pandas, SciPy, NumPy, Scikit-Learn, Plot.ly, and BioPython)
Perl: Intermediate+
R: Intermediate
PHP: Beginner

Database

MySQL: Intermediate

Advanced GNU/Linux

Publications

2022

Sarah L Schwartz, Lily Momper, Luiz Thiberio Rangel, Cara Magnabosco, Jan P Amend, Gregory P Fournier. Novel nitrite reductase domain structure suggests a chimeric denitrification repertoire in the phylum Chloroflexi. MicrobiologyOpen. 2022.

2021

L. Thiberio Rangel, Shannon M. Soucy, João Carlos Setubal, Gregory P. Fournier. An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets. Genome Biology and Evolution. 2021.

GP Fournier, KR Moore, LT Rangel, JG Payette, L Momper, T Bosak. The Archean origin of oxygenic photosynthesis and extant cyanobacterial lineages. Proceedings of the Royal Society B. 2021.

2020

Taylor Wade, L. Thiberio Rangel, Soumya Kundu, Gregory P. Fournier, Mukul S. Bansal. Assessing the Accuracy of Phylogenetic Rooting Methods on Prokaryotic Gene Families. PLOS One. 2020.

2019

Luiz Thiberio Rangel, Gregory P. Fournier. Fast-evolving alignment sites are highly informative for reconstructions of deep Tree of Life phylogenies. bioRxiv. 2019; 835504.

Luiz Thiberio Rangel, Jeremiah Marden, Sophie Colston, João Carlos Setubal, Joerg Graf, Johann Peter Gogarten. Identification and characterization of putative Aeromonas spp. T3SS effectors. PlosOne. 2019 Jun 4; 14(6):e0214035

José SL Patané, Joaquim Martins, Luiz Thiberio Rangel, José Belasque, Luciano A Digiampietri, Agda Paula Facincani, Rafael Marini Ferreira, Fabrício José Jaciani, Yunzeng Zhang, Alessandro M Varani, Nalvo F Almeida, Nian Wang, Jesus A Ferro, Leandro M Moreira, João C Setubal. Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses. BMC genomics. 2019 Sep 9; 20(1):700

2017

Wang N, Pierson EA, Setubal JC, Xu J, Levy JG, Zhang Y, Li J, Rangel LT, Martins J Jr. The Candidatus Liberibacter-Host Interface: Insights into Pathogenesis Mechanisms and Disease Control. Annual Reviews Phytopathology. 2017 Aug 4; 55:451-482

2014

Wulff NA, Zhang S, Setubal JC, Almeida NF, Martins EC, Harakava R, Kumar D, Rangel LT, Foissac X, Bové JM, Gabriel DW. The Complete Genome Sequence of 'Candidatus Liberibacter americanus', Associated with Citrus Huanglongbing. Mol Plant Microbe Interact. 2014 Feb; 27(2):163-76

2013

Rangel LT, Novaes J, Durham AM, Madeira AMBN, Gruber A. The Eimeria Transcript DB: an integrated resource for annotated transcripts of protozoan parasites of the genus Eimeria. Database (Oxford). 2013 Feb 14;2013:bat006

2012

Novaes J*, Rangel LTLD*, Ferro M, Abe RY, Manha AP, de Mello JC, Varuzza L, Durham AM, Madeira AMBN, Gruber A. A comparative transcriptome analysis reveals expression profiles conserved across three Eimeria spp. of domestic fowl and associated with multiple developmental stages. International Journal of Parasitology. 2012 Jan;42(1):39-48.
*Both authors contributed equally to the work.

Hobbies

Electric guitar

References

Available upon request