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L. Thibério Rangel, Ph.D.

Email:
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My research is based on applying comparative genomics and phylogenomics approaches on large prokaryotic data sets to improve our understand of Horizontal Gene Transfer mechanisms and its impact on evolution.

I have B.Sc. in Biological Sciences (UFPB) and a Ph.D. in Bioinformatics (USP), and have been trained as a bioinformatician since early undergrad research projects, mainly focused on comparitive genomics. Currently, I am a Postdoctoral Associate at MIT, working with Dr. Greg Fournier, focusing on how we can use HGT inferences to improve time calibrations along the Tree of Life!

My research experiences comprehends:
  • Comparative genomics;
  • Development of Bioinformatic tools;
  • Phylogenomics and Molecular evolution methods;
  • Statistical analysis of biological data;
  • Statistical clustering;
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

Postdoctoral appointments

Postdoctoral Associate

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

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

Supplementary education

Summer School on Networks and Evolution

Roscoff, Fr
Jul 3 - Jul 9, 2016

Workshop on Molecular Evolution

Marine Biological Laboratory, Woods Hole, MA, USA
Jul 27 - Aug 6, 2014
url: https://molevol.mbl.edu

5th Annual EuPathDB Workshop

University of Georgia, Athens, GA, USA
Jun 6 - Jun 9, 2010
url: http://workshop.eupathdb.org

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

Research interests

Genomics
Protein annotation
Molecular evolution
Horizontal gene transfer
Phylogenomic networks

Publications

2020

L. Thiberio Rangel, Shannon M. Soucy, João Carlos Setubal, Gregory P. Fournier. Non-phylogenetic identification of co-evolving genes for reconstructing the archaeal Tree of Life. bioRxiv. 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. Annu Rev Phytopathol. 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. Int J Parasitol. 2012 Jan;42(1):39-48.
*Both authors contributed equally to the work.

Posters

[9] Rangel LT, Setubal JC. Gene Transfer and Nitrogen Fixation Genes in Gamma- and Beta-Proteobacteria. RECOMB Comparative Genomics, 2013.

[8] Rangel LTLD, Setubal JC, Wu F, Lin H e Mohamed N. Analysis of Proteobacterial genomes using Phylogenomic Networks. Brazilian Symposium on Bioinformátics, 2012.

[7] Amgarten D, Rangel LTLD, Durham AM, Gruber A. Desenvolvimento de um Componente de anotação automática de vias metabólicas KEGG para a plataforma EGene. SIICUSP, 2010.

[6] Rangel LTLD, Durham AM,Gruber, A . Enriched annotation and functional assignment of proteins of Eimeria spp.: guilty by orthology. X-Meeting, 2010.

[5] Ferro M, Yamamoto R, Rangel LTLD, Durham AM, Gruber, A . EGene 2: a generic and modular platform for automated sequence processing and annotation. X-Meeting, 2009.

[4] Rangel LTLD, Rocha PKL, Paschoal AR, Vitorello CBM, Araújo DAM, Rego TG. GIAnT: Genomic Island Analyzer Tool. X-Meeting, 2008.

[3] Rocha PKL, Rangel LTLD, Paschoal AR, Vitorello CBM, Araújo DAM, Rego TG. Quantitative analysis of genomic islands in Bacteria. X-Meeting, 2008.

[2] Rocha PKL, Rangel LTLD, Vitorello CBM, Araújo DAM, Rego TG. Identificação e caracterização de ilhas genômicas em bactérias do gênero Mycoplasma. Congresso Brasileiro de Genéttica, 2008.

[1] Bezerra AV, Martins AB, Souza HDN, Rangel LTLD, Rocha PKL, Araújo DAM. Avaliação do potencial leishmaniostático do composto natural isolado quercetina sobre Leishmania chagasi, Congresso Brasileiro de Parasitologia. 2007.

Hobbies

Electric guitar

References

Available upon request