Rodrigo de Paula Baptista

235 Bedford Drive Athens, GA 30606

rodrigopbaptista@gmail.com • 706-224-6542

Bsc Biomedical Sciences | PhD Bioinformatics

RESEARCH INTERESTS

Genome Evolution; Genomics; Transcriptomics; Copy Number Variation; Phylogenomics;

Population Genetics; Infectious diseases; Epidemiology.

EDUCATION

Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil August 2014
Doctor of Philosophy, Bioinformatics
Thesis: “Bioinformatics approaches applied in the study of Trypanosoma cruzi population
structure.

Universidade FUMEC, Belo Horizonte, MG, Brazil December 2008

Bachelor of Sciences, Biomedical sciences
Dissertation: “Molecular characterization of T. cruzi isolates from chagasic patients from Minas
Gerais and Rio Grande do Norte Brazilian states”

RESEARCH EXPERIENCE

Center for Tropical & Emerging Global Diseases, November 2015 – Present
The University of Georgia
Postdoctoral Research and Teaching Associate
• Performed the new Cryptosporidium mice infection model, C. tyzzeri, genome assembly
and annotation
• Revisited and improved the genome annotation of two human infection Cryptosporidium
reference species (C. parvum and C. hominis)
• Updated the structural and function annotation of Cryptosporidium using AUGUSTUS,
SNAP, Genemark-ES, MAKER, WebApollo2 and Interproscan
• Analyzed gene copy number variation among different Cryptosporidium species. Applied
the same pipeline to predict a targeted gene copy number in Toxoplasma gondii
• Maintained a Webapollo2 server
• Developed a bash command-line based user-friendly SNP-call analysis pipeline, using
GATK, FreeBayes, Samtools
• Performed for the first time the recombination analysis in Cryptosporidium using the
recombination detection tool Redhorse and some “in house” developed parsing tools
• Analyzed genomic and transcriptomic data of several Cryptosporidium species
• Performed different genome assembly methods using PacBio and Nanopore long reads
• Performed Mass Spectrometry computational analysis
• Performed Metagenomics analysis using Metaphlan, Qiime, metAMOS, TAG.ME.
Department of Parasitology, September 2014-October-2015
Universidade Federal de Minas Gerais
Postdoctoral Research Associate
• Analyzed and characterized the sequence diversity and generation mechanism in the largest
Trypanosoma cruzi gene families encoding surface proteins
• Assisted and performed Leishmania (Viannia) peruviana and Leishmania (Viannia)
braziliensis genome assembly and comparative genomics analysis
• Performed the bioinformatics analysis of molecular mimicry between Plasmodium vivax
and human erythrocyte membrane proteins, to explain a putative mechanism contributing
to anemia
• Contributed in the bioinformatics analysis of chromosomal copy number variation in
distinct Trypanosoma cruzi strains, to access their differential level of genomic plasticity;
• Assembled several Trypanosomatid sequences using different methods and sequencing
platforms, such as Illumina, ABI Sanger, and Roche 454
• Member of an administrative team to maintain two Linux Computer clusters
• Participated for two consecutive years in the university team that competed in the
International Genetic Engineering Machine (IGEM) competition, working with
computational modeling and synthetic biology methods
• Co-Advised M.Sc Cláudia Barbosa Assunção, in the dissertation “Caracterização
computational de Proteínas hipotéticas conservadas de T. cruzi / Computational
characterization of T. cruzi conserved hypothetical proteins”, in which was defended in the
Universidade Federal de Minas Gerais, Department of Bioinformatics, in 2016

Department of Biochemistry and Immunology, August 2007 – August 2014

Universidade Federal de Minas Gerais

PhD student August 2010 – August 2014

• Performed an evolutionary study of different T. cruzi DTU-II isolates from several
locations in Brazil, using different microsatellite markers and found evidences that
recombination events are more frequent than previously described in the species
• Maintained in culture, selected, cloned and extracted DNA from a T. cruzi DTU-III strain
found in a human patient
• Developed a hybrid assembly pipeline to deal with high repetitive genomes using just short
reads
• Assembled the first whole genome sequence of a T. cruzi DTU-III, using Illumina short
reads. Also performed an annotation transfer using a rapid annotation transfer tool (RATT)
• Performed an evolutionary analysis using comparative genomics, gene Orthology
(OrthoMCL), Maximum likelihood (PhyML), Bayesian analysis (BEAST)
• Developed a sequence clusterization method based in Singular-value decomposition, and
analyzed the data using uni and multivariate statistics in, SPSS, Matlab and R
• Students’ titular representative in the Bioinformatics Collegiate committee (2011-2013)
Technologist January 2009 – July 2010
• Performed capillary Sanger genomic sequencing of three fungi species that cause rust
coffee, eucalyptus and corn, for Rede Genoma Minas consortium (RGMG)
• Prepared shotgun sequence libraries, miniprep and sequence reactions for Sanger capillary
sequences
• Maintained and operated MegaBACE 1000 Sequencing System equipment
• Assembled sanger sequences for the project submission

Undergrad student August 2007 – December 2009

• Performed and analyzed molecular characterization from several isolates from T. cruzi
from different Brazilian states. (PCR, RFLP-PCR, Long-PCR)
• Developed of a multiplex PCR-based strategy involving the bidirectional PCR
amplification of specific alleles (Bi-PASA) targeted in the mitochondrial T. cruzi gene
NADH dehydrogenase subunit 1, to simplify, make faster and cheaper the characterization
of some different types of T. cruzi (DTUs);
• Detected and performed Microsatellite analysis of several loci, using an Automatic Laser
Fluorescence DNA sequencer (ALF), and some bioinformatics tools such as tandem repeat
finder

TEACHING EXPERIENCE

Applied Genomics Analysis (BINF-8940) Fall 2018 - Present

Institute of Bioinformatics, University of Georgia
• Instructor of the whole semester
• Topics Covered: basic Linux, accessing an HPC
cluster from a terminal, Genome assembly,
annotation, Comparative genomics, SNP analysis,
Transcriptome assembly and differential expression
analysis.

2-day UGA EupathDB workshop Teaching Assistant August 2016

CTEGD, The University of Georgia
• Guided students through the practical exercises;
• Answered student’s questions.

Mathematical Modeling of Metabolic Networks Febuary 2015

I Summer course of Biological Engineering, Department of Bioinformatics, Universidade Federal
de Minas Gerais
• Created, revised and presented a lecture about Metabolic Networks;
• Coordinated and presented a practical lecture about constructing artificial DNA segments
using a synthetic biology tool (GeneDesiner 2.0);

Molecular Biology Teaching Assistant February – June 2009

Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais
 • Guided undergraduate students through Molecular Biology exercises;
• Assigned and graded tests;

PUBLICATIONS

Baptista R.P., D'Avila D.A., Segatto M., do Valle I.F., Franco G.R, Valadares H.M., Gontijo E.D.,
Galvao L.M., Pena S.D., Chiari E., Machado C.R. and Macedo A.M. (2014). "Evidence of
substantial recombination among Trypanosoma cruzi II strains from Minas Gerais." Infect Genet
Evol 22: 183-191.

Carranza J. C., Valadares H.M., D'Avila D.A., Baptista R.P., Moreno M., Galvao L.M., Chiari
E., Sturm N.R., Gontijo E.D., Macedo A.M and Zingales B. (2009). "Trypanosoma cruzi
maxicircle heterogeneity in Chagas disease patients from Brazil." Int J Parasitol 39(9): 963-973.

Ferreira K. A., Fajardo E. F., Baptista R. P., Macedo A. M., Lages-Silva E., Ramirez L.E. and
Pedrosa A. L. (2014). "Species-specific markers for the differential diagnosis of Trypanosoma
cruzi and Trypanosoma rangeli and polymorphisms detection in Trypanosoma rangeli." Parasitol
Res 113(6): 2199-2207.

Reis-Cunha J. L., Rodrigues-Luiz G. F., Valdivia H. O., Baptista R. P., Mendes T. A., de Morais
G. L., Guedes R., Macedo A. M., Bern C., Gilman R. H., Lopez C. T., Andersson B., Vasconcelos
A. T. and Bartholomeu D. C. (2015). "Chromosomal copy number variation reveals differential
levels of genomic plasticity in distinct Trypanosoma cruzi strains." BMC Genomics 16: 499.

Valdivia H. O., Reis-Cunha J. L., Rodrigues-Luiz G. F., Baptista R. P., Baldeviano G. C., Gerbasi
R. V., Dobson D. E., Pratlong F., Bastien P., Lescano A. G., Beverley S. M. and Bartholomeu D.
C. (2015). "Comparative genomic analysis of Leishmania (Viannia) peruviana and Leishmania
(Viannia) braziliensis." BMC Genomics 16: 715.

Dhara A., Baptista R.P., Kissinger J.C., Snow E.C. and Sinai A.P (2017). “Ablation of an OTU-
family deubiquitinase exposes the underlying regulation governing the plasticity of cell cycle
progression in Toxoplasma gondii.” MBio 8 (6), e01846-17.

Baptista, R.P., Reis-Cunha J.L, DeBarry J.D., Chiari E., Kissinger J.C., Bartholomeu D.C. and
Macedo A.M. (2018). “Assembly of highly-repetitive genomes using short reads: The genome of
DTU III Trypanosoma cruzi strain 231.” Mgen.

Quaresma P., de Brito C.F.A., Rugani J.M., Freire J.M., Baptista R.P., Moreno E.C., Gontijo
R.C., Rego F.D., Diniz J.E., Melo M.N. and Gontijo C.M.F. (2018) “Distinct genetic profiles of
Leishmania (Viannia) braziliensis associates to clinical variations in cutaneous leishmaniasis
patients from an endemic area in Brazil” Parasitology 1-9.

Fuselli S., Baptista R.P., Panziera A., Magi A., Guglielmi S., Tonin R., Benazzo A., Bauzer L.G.,
Mazzoni C.J. and Bertorelle G. (2018) “High-throughput NGS and long read MinION nanopore
sequencing: a hybrid approach for MHC genotyping in the non-model vertebrate Alpine chamois
(Rupicapra rupicapra)” Heredity.
Mourão L.C., Baptista R.P., Almeida Z., Grynberg P., Pucci M.M., Castro-Gomes T., Fontes
C.J.F., Silva-Pereira R., Bemquerer M.P. and Braga E. (2018) “Molecular mimicry between
Plasmodium vivax and human red blood cell proteins: a possible mechanism underlying anemia”
Scientific Reports.

Reis-Cunha J.L., Baptista R.P., Rodrigues-Luiz G.F., Valdivia H.O., Almeida L.V., Cardoso
M.S., Davila D.A., Cunha Dias F.H., Galvao L.M.C., Chiari E., Cerqueira G.C., Bartholomeu D.C.
(2018) “Whole genome sequencing of Trypanosoma cruzi field isolates reveals extensive genomic
variability and complex aneuploidy patterns within TcII DTU” BMC Genomics.

Sateriale A., Slapeta Y., Baptista R.P., Engiles J.B., Gullicksrud J.A., Helbert G., Brooks C.F.,
Kugler E.M., Kissinger J.C., Hunter C.A. and Striepen B. (2019) “A Genetically Tractable,
Natural Mouse Model of Cryptosporidiosis Offers Insights into Host Protective Immunity” Cell
Host & Microbe.

Baptista R.P. and Kissinger J.C. (2019) “Is reliance upon an inaccurate genome sequence
sabotaging your experiments?” Plos Pathogens Pearls. (Accepted)

Maboni G., Krimer P., Baptista R.P., Lorton A., Anderson C. and Sanchez S. (2019). “Laboratory
diagnostics, phylogenetic analysis and clinical outcome of a subcutaneous Mycoleptodiscus
indicus infection in an immunocompetent cat” BMC Veterinary Research (Accepted)

Submitted

Florentin A., Stephens D.R., Brooks C.F., Baptista R.P, Muralidharan V (2019). “The Clp
proteolytic system acts as an essential nexus for Plasmodium plastid biogenesis” eLife.

Silva S.O., Reis-Cunha J.L, Baptista R.P., Castro B.R., Macedo A.M., Bartholomeu D.C. and
Melo M.N. (2019). “Genetic diversity of Leishmania (Leishmania) infantum (MON-1) revealed
by a new set of microsatellite markers” Experimental Parasitology.

In Prep

Baptista R.P., Li Y., Sateriale A., Ansell B., Jex A., Sanders M., Brooks K., Tracey A., Berriman
M., Striepen B., Cotton J.A. and Kissinger J.C. (2019). “Consistent, comparative and evidence-
based genome annotation and re-annotation for the closely-related species, Cryptosporidium
parvum, C. hominis and C. tyzzeri.” Genome Research.

Colon B., Baptista R.P. and Kyle D. (2019) “Resistant Naegleria fowleri elucidates potential
targets for drug discovery” International Journal for Parasitology.

Namasivayam S., Xiao W., Baptista R.P., Hall E.M, Doggett J.S., Troell K. and Kissinger J.C.
(2019) “The highly-unusual yet evolutionarily conserved fragmented mitochondrial genome of the
coccidian, Toxoplasma gondii” PNAS.
Wang W., Baptista R.P., Peng D., Li Y., Mining T., Kissinger J.C. and Tarleton R.L. (2019) “Two
High-quality Reference Genome Assemblies for Trypanosoma cruzi TcI and TcII Strains”.

Louis E.P., Etheridge M., Baptista R.P. and Etheridge R.D. (2019). “Role of a Secreted Effector
of Toxoplasma gondii in Modulating the Host Cell Cycle”.

Butler J.H., Merino E.F., Baptista R.P., Okoro J.I, Scales R.M., Rosenthal P.J., Cooper R.A.,
Kissinger J.C., Yue J., Zhou B. and Cassera M.B. (2019). “Mutations in Plasmodium falciparum
Pro-drug Activation and Resistance Esterase Mediates Resistance to a Sub-class of Sesquiterpene
Dimer Antimalarial Natural Products”

Li Y., Baptista R.P. and Kissinger J.C. (2019). “Non-coding RNAs in the apicomplexan parasites:
an update” Trends in Parasitology

CONFERENCES & WORKSHOPS

2019 29th Molecular Parasitology & Vector Biology Symposium (Symposium)

2018 2018 (29th) Annual Molecular Parasitology Meeting (Conference)
2018 28th Molecular Parasitology & Vector Biology Symposium (Symposium)
2017 American Society of Tropical Medicine and Hygiene 66th Annual meeting (Conference)
2017 UGA Institute of Bioinformatics Symposium: Parsing the Microbiome (Symposium)
2017 27th Annual Molecular Parasitology & Vector Biology Symposium (Symposium)
2016 American Society of Tropical Medicine and Hygiene 65th Annual meeting (Conference)
2016 26th Annual Molecular Parasitology & Vector Biology Symposium (Symposium)
2015 International Genetically Engineered Machine Competition (Conference / Competition)
2015 XXVI Molecular Parasitology Meeting (Conference)
2014 International Genetically Engineered Machine Competition (IGEM). (Conference /
Competition)
2014 V Encontro de Pesquisa em Parasitologia: Novas Abordagens para Antigos. (Poster Section
Evaluator/Congress).
2014 VII Seminário da Química na X Semana de Ciência & Tecnologia do CEFET-MG.
"Synthetic Biology: Biology from the Engineering perspective". (Speaker)
2013 XXIV Molecular Parasitology Meeting (Congress).
2013 Institute of Bioinformatics State-of-the-Art Next Generation Sequence Analysis
Symposium. (Symposium).
2012 XI International Conference on Molecular Epidemiology and evolutionary Genetics of
infectious Diseases (Congress).
2012 XXVIII Annual Meeting of the Brazilian Society of Protozoology/ XXXIX Annual
Meeting on Basic Research in Chagas Disease (Congress).
2011 7th international conference of the Brazilian Association for Bioinformatics and
Computational Biology and 3rd International Conference of the IberoAmerican Society for
Bioinformatics (Congress)
2011 XXVII Annual Meeting of the Brazilian Society of Protozoology/ XXXVIII Annual
Meeting on Basic Research in Chagas Disease (Congress).
2010 XXVI Annual Meeting of the Brazilian Society of Protozoology/ XXXVII Annual Meeting
on Basic Research in Chagas Disease (Congress).
2010 6th international conference of the Brazilian Association for Bioinformatics and
Computational Biology (Congress).
2009 XIII internacional congress of protistology/XXV Annual Meeting of the Brazilian Society
of Protozoology/XXXVI Annual Meeting on basic Research in Chagas' Disease (Congress).
2009 Simpósio Internacional comemorativo do centenário da descoberta da doença de Chagas
(Symposium).
2008 54º Congresso Brasileiro de Genética (Congress).
2008 XXIV Reunião Anual da Sociedade Brasileira de Protozoologia / XXXV Reunião Anual
sobre pesquisa básica em Doença de Chagas (Congress).
2008 11º Encontro Regional de Biomedicina (Meeting).
2008 IX Encontro de Pesquisa do Instituto de Ciências Biológicas/ IV Encontro Anual de
Pesquisa em Bioquímica e Imunologia (Meeting).
2007 2º Congresso Mineiro de Alergia e Imunologia Clínica/ Encontro do Grupo Brasileiro de
Imunologia Clínica (Congress).
2007 10º Encontro Regional de Biomedicina (Meeting).
2006 9º Encontro regional de Biomedicina (Meeting).
2005 2ª Semana do Conhecimento da Facudade de Ciências da Saúde – FUMEC (Seminar).
2005 III Encontro Mineiro de Biomedicina (Meeting).
2001 XII Seminário do IPEC. A fisiologia do Coração (Seminar).

GRANTS & FUNDING

Co-Investigator
2019-2021 NIH R21 AI144779-01A1 two-year grant. Detailed analysis of Cryptosporidium
non-coding gene expression $275,000

Key personnel
2016 Bill & Melinda Gates Foundation. Enhanced Cryptosporidium reference genome sequence
resources. $114,975
2011 FAPEMIG DEMANDA UNIVERSAL APQ-01397-11 three-year grant. The goal of this
project is to develop molecular tools suitable for the six T. cruzi DTU identification and
for phylogenetic and population studies based in molecular markers. R$ 48,000

REVIEWER FOR Acta Tropica, Journal of Molecular Evolution, Molecular Genetics

and Genomics, GigaScience, PLOS Neglected Tropical Diseases
and Microbial Genomics

LANGUAGES Portuguese, English: Fluent, professional verbal and written

communication skills
Spanish: Advanced, informal verbal and written communication
skills
German: Basic

COMPUTATIONAL Bash, Perl, Python, R, MySQL and PHP.

SKILLS
PROFESSIONAL ORGANIZATIONS

American Heart Association 2017-Present

Sociedade Brasileira de Protozoologia 2008-2012
Associação Brasileria de Bioinformática e Biologia Computacional 2010-2011

HONORS & AWARDS

• Best Education and Public Engagement, overgrad at the International Genetically

Engineered Machine competition (2015);
• CNPq Postdoctoral junior fellowship (2014);
• VII Prêmio Carlos Roberto Rúbio de Iniciação Científica (Best oral presentation), Instituto
de Biociências – Unesp (2008);
• Best Poster presentation at the 2ª Semana do Conhecimento da Faculdade de Ciências da
Saúde - Universidade FUMEC (2005).