Felipe Pereira, PhD


Felipe is a Bioinformatician with a Computer Science background. He received his Ph.D. degree at Minas Gerais, Brazil, in 2019. In his Ph.D. thesis, he studied host-pathogen interaction in important zoonotic fish-pathogenic bacteria. He had experience as a teacher assistant in Programming Languages and Software Engineering and he worked in the National Reference Laboratory of the Brazilian Ministry of Agriculture using different types of omics technologies, such as transcriptomics and proteomics. His main interest is to integrate data from different technologies and work with big data science. He has begun as a Bioinformatician in Profs. Grinberg and Willian Seeley’s labs on May 1st of 2021, and his efforts are linked to Single Nuclei/Bulk RNA sequencing data processing, data integration, and statistical analysis.


Frontotemporal lobar degeneration targets brain regions linked to expression of recently evolved genes.

Pasquini L, Pereira FL, Seddighi S, Zeng Y, Wei Y, Illán-Gala I, Vatsavayai SC, Friedberg A, Lee AJ, Brown JA, Spina S, Grinberg LT, Sirkis DW, Bonham LW, Yokoyama JS, Boxer AL, Kramer JH, Rosen HJ, Humphrey J, Gitler AD, Miller BL, Pollard KS, Ward ME, Seeley WW

FTLD targets brain regions expressing recently evolved genes.

Pasquini L, Pereira FL, Seddighi S, Zeng Y, Wei Y, Illán-Gala I, Vatsavayai SC, Friedberg A, Lee AJ, Brown JA, Spina S, Grinberg LT, Sirkis DW, Bonham LW, Yokoyama JS, Boxer AL, Kramer JH, Rosen HJ, Humphrey J, Gitler AD, Miller BL, Pollard KS, Ward ME, Seeley WW

Synergic Effect of Brachyspira hyodysenteriae and Lawsonia intracellularis Coinfection: Anatomopathological and Microbiome Evaluation.

Daniel AGS, Pereira CER, Dorella F, Pereira FL, Laub RP, Andrade MR, Barrera-Zarate JA, Gabardo MP, Otoni LVA, Macedo NR, Correia PA, Costa CM, Vasconcellos AO, Wagatsuma MM, Marostica TP, Figueiredo HCP, Guedes RMC

Transmission of Escherichia coli Causing Pyometra between Two Female Dogs.

Xavier RGC, Santana CH, da Silva PHS, Aburjaile FF, Pereira FL, Figueiredo HCP, Freitas PMC, Santos RL, Silva ROS

Rainwater Charitable Foundation criteria for the neuropathologic diagnosis of progressive supranuclear palsy.

Roemer SF, Grinberg LT, Crary JF, Seeley WW, McKee AC, Kovacs GG, Beach TG, Duyckaerts C, Ferrer IA, Gelpi E, Lee EB, Revesz T, White CL, Yoshida M, Pereira FL, Whitney K, Ghayal NB, Dickson DW

Caspase-6-cleaved tau is relevant in Alzheimer's disease and marginal in four-repeat tauopathies: diagnostic and therapeutic implications.

Theofilas P, Piergies AMH, Oh I, Lee YB, Li SH, Pereira FL, Petersen C, Ehrenberg AJ, Eser RA, Ambrose AJ, Chin B, Yang T, Khan S, Ng R, Spina S, Seeley WW, Miller BL, Arkin MR, Grinberg LT

Subcortical Neuronal Correlates of Sleep in Neurodegenerative Diseases.

Oh JY, Walsh CM, Ranasinghe K, Mladinov M, Pereira FL, Petersen C, Falgàs N, Yack L, Lamore T, Nasar R, Lew C, Li S, Metzler T, Coppola Q, Pandher N, Le M, Heuer HW, Heinsen H, Spina S, Seeley WW, Kramer J, Rabinovici GD, Boxer AL, Miller BL, Vossel K, Neylan TC, Grinberg LT

First report of infectious spleen and kidney necrosis virus in Nile tilapia in Brazil.

Figueiredo HCP, Tavares GC, Dorella FA, Rosa JCC, Marcelino SAC, Pierezan F, Pereira FL

Re-sequencing and optical mapping reveals misassemblies and real inversions on Corynebacterium pseudotuberculosis genomes.

Sousa TJ, Parise D, Profeta R, Parise MTD, Gomide ACP, Kato RB, Pereira FL, Figueiredo HCP, Ramos R, Brenig B, Costa da Silva ALD, Ghosh P, Barh D, Góes-Neto A, Azevedo V

Streptococcus agalactiae Sequence Type 283 in Farmed Fish, Brazil.

Leal CAG, Queiroz GA, Pereira FL, Tavares GC, Figueiredo HCP

Delineation of the pan-proteome of fish-pathogenic Streptococcus agalactiae strains using a label-free shotgun approach.

Tavares GC, Pereira FL, Barony GM, Rezende CP, da Silva WM, de Souza GHMF, Verano-Braga T, de Carvalho Azevedo VA, Leal CAG, Figueiredo HCP

Transcriptome and Proteome of Fish-Pathogenic Streptococcus agalactiae Are Modulated by Temperature.

Tavares GC, Carvalho AF, Pereira FL, Rezende CP, Azevedo VAC, Leal CAG, Figueiredo HCP

Complete genome sequencing of sixteen Francisella noatunensis subsp. orientalis isolates: A genomic approach for molecular characterization and spread dynamics of this clonal population.

Pereira FL, Gonçalves LA, Tavares GC, Soares SC, Dorella FA, de Carvalho AF, Leibowitz MP, Leal CAG, Azevedo VAC, Figueiredo HCP

Comparative proteomic analysis of four biotechnological strains Lactococcus lactis through label-free quantitative proteomics.

Silva WM, Sousa CS, Oliveira LC, Soares SC, Souza GFMH, Tavares GC, Resende CP, Folador EL, Pereira FL, Figueiredo H, Azevedo V

First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico.

Parise D, Parise MTD, Viana MVC, Muñoz-Bucio AV, Cortés-Pérez YA, Arellano-Reynoso B, Díaz-Aparicio E, Dorella FA, Pereira FL, Carvalho AF, Figueiredo HCP, Ghosh P, Barh D, Gomide ACP, Azevedo VAC

Gut microbiome modulation during treatment of mucositis with the dairy bacterium Lactococcus lactis and recombinant strain secreting human antimicrobial PAP.

Carvalho R, Vaz A, Pereira FL, Dorella F, Aguiar E, Chatel JM, Bermudez L, Langella P, Fernandes G, Figueiredo H, Goes-Neto A, Azevedo V

Mutation of the Surface Layer Protein SlpB Has Pleiotropic Effects in the Probiotic Propionibacterium freudenreichii CIRM-BIA 129.

do Carmo FLR, Silva WM, Tavares GC, Ibraim IC, Cordeiro BF, Oliveira ER, Rabah H, Cauty C, da Silva SH, Canário Viana MV, Caetano ACB, Dos Santos RG, de Oliveira Carvalho RD, Jardin J, Pereira FL, Folador EL, Le Loir Y, Figueiredo HCP, Jan G, Azevedo V

Transcriptome analysis of Corynebacterium pseudotuberculosis biovar Equi in two conditions of the environmental stress.

Gomide ACP, Ibraim IC, Alves JTC, de Sá PG, de Oliveira Silva YR, Santana MP, Silva WM, Folador EL, Mariano DCB, de Paula Castro TL, Barbosa S, Dorella FA, Carvalho AF, Pereira FL, Leal CAG, Figueiredo HCP, Azevedo V, Silva A, Folador ARC

Label-free proteome of water buffalo (Bubalus bubalis) seminal plasma.

Brito MF, Auler PA, Tavares GC, Rezende CP, Almeida GMF, Pereira FL, Leal CAG, Moura AA, Figueiredo HCP, Henry M

Comparative genomic analysis between Corynebacterium pseudotuberculosis strains isolated from buffalo.

Viana MVC, Figueiredo H, Ramos R, Guimarães LC, Pereira FL, Dorella FA, Selim SAK, Salaheldean M, Silva A, Wattam AR, Azevedo V

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology.

Mariano DC, Pereira FL, Aguiar EL, Oliveira LC, Benevides L, Guimarães LC, Folador EL, Sousa TJ, Ghosh P, Barh D, Figueiredo HC, Silva A, Ramos RT, Azevedo VA

Complete Genome Sequence of the Attenuated Corynebacterium pseudotuberculosis Strain T1.

Almeida S, Loureiro D, Portela RW, Mariano DC, Sousa TJ, Pereira FL, Dorella FA, Carvalho AF, Moura-Costa LF, Leal CA, Figueiredo HC, Meyer R, Azevedo V

Whole-Genome Sequence of Corynebacterium auriscanis Strain CIP 106629 Isolated from a Dog with Bilateral Otitis from the United Kingdom.

Tiwari S, Jamal SB, Oliveira LC, Clermont D, Bizet C, Mariano D, de Carvalho PV, Souza F, Pereira FL, de Castro Soares S, Guimarães LC, Dorella F, Carvalho A, Leal C, Barh D, Figueiredo H, Hassan SS, Azevedo V, Silva A

Complete genome sequence of Streptococcus agalactiae strain GBS85147 serotype of type Ia isolated from human oropharynx.

de Aguiar EL, Mariano DC, Viana MV, Benevides Lde J, de Souza Rocha F, de Castro Oliveira L, Pereira FL, Dorella FA, Leal CA, de Carvalho AF, Santos GS, Mattos-Guaraldi AL, Nagao PE, de Castro Soares S, Hassan SS, Pinto AC, Figueiredo HC, Azevedo V

Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002.

Mariano DC, Sousa Tde J, Pereira FL, Aburjaile F, Barh D, Rocha F, Pinto AC, Hassan SS, Saraiva TD, Dorella FA, de Carvalho AF, Leal CA, Figueiredo HC, Silva A, Ramos RT, Azevedo VA

Complete genome sequences of Francisella noatunensis subsp. orientalis strains FNO12, FNO24 and FNO190: a fish pathogen with genomic clonal behavior.

Gonçalves LA, de Castro Soares S, Pereira FL, Dorella FA, de Carvalho AF, de Freitas Almeida GM, Leal CA, Azevedo V, Figueiredo HC

The genome anatomy of Corynebacterium pseudotuberculosis VD57 a highly virulent strain causing Caseous lymphadenitis.

Almeida S, Tiwari S, Mariano D, Souza F, Jamal SB, Coimbra N, Raittz RT, Dorella FA, Carvalho AF, Pereira FL, Soares Sde C, Leal CA, Barh D, Ghosh P, Figueiredo H, Moura-Costa LF, Portela RW, Meyer R, Silva A, Azevedo V

Complete genome sequence of Peptoclostridium difficile strain Z31.

Pereira FL, Oliveira Júnior CA, Silva ROS, Dorella FA, Carvalho AF, Almeida GMF, Leal CAG, Lobato FCF, Figueiredo HCP

Draft Genome Sequences of Two Pathogenic Corynebacterial Species Isolated from Cows.

Guimarães LC, Lopes T, Ramos RT, Carneiro AR, Cavalcante AL, Barreto D, de Sá PC, Veras AA, Rocha FS, Bagano P, Pereira FL, Dorella FA, Leal CA, Carvalho AF, Bizet C, Guiso N, Badell E, Figueiredo HC, Azevedo V, Silva A

Complete Genome Sequence of Corynebacterium pseudotuberculosis Viscerotropic Strain N1.

Loureiro D, Portela RW, Sousa TJ, Rocha F, Pereira FL, Dorella FA, Carvalho AF, Menezes N, Macedo ES, Moura-Costa LF, Meyer R, Leal CA, Figueiredo HC, Azevedo V

Comparative genome analysis of Weissella ceti, an emerging pathogen of farm-raised rainbow trout.

Figueiredo HC, Soares SC, Pereira FL, Dorella FA, Carvalho AF, Teixeira JP, Azevedo VA, Leal CA

Draft Genome Sequences of Two Species of "Difficult-to-Identify" Human-Pathogenic Corynebacteria: Implications for Better Identification Tests.

Pacheco LG, Mattos-Guaraldi AL, Santos CS, Veras AA, Guimarães LC, Abreu V, Pereira FL, Soares SC, Dorella FA, Carvalho AF, Leal CG, Figueiredo HC, Ramos JN, Vieira VV, Farfour E, Guiso N, Hirata R, Azevedo V, Silva A, Ramos RT

MapRepeat: an approach for effective assembly of repetitive regions in prokaryotic genomes.

Mariano DC, Pereira FL, Ghosh P, Barh D, Figueiredo HC, Silva A, Ramos RT, Azevedo VA

Genome Sequence of Corynebacterium ulcerans Strain FRC11.

Benevides Lde J, Viana MV, Mariano DC, Rocha Fde S, Bagano PC, Folador EL, Pereira FL, Dorella FA, Leal CA, Carvalho AF, Soares Sde C, Carneiro A, Ramos R, Badell-Ocando E, Guiso N, Silva A, Figueiredo H, Azevedo V, Guimarães LC

Genome Sequence of Corynebacterium ulcerans Strain 210932.

Viana MV, de Jesus Benevides L, Batista Mariano DC, de Souza Rocha F, Bagano Vilas Boas PC, Folador EL, Pereira FL, Alves Dorella F, Gomes Leal CA, Fiorini de Carvalho A, Silva A, de Castro Soares S, Pereira Figueiredo HC, Azevedo V, Guimarães LC

Genome Sequence of Lactococcus lactis subsp. lactis NCDO 2118, a GABA-Producing Strain.

Oliveira LC, Saraiva TD, Soares SC, Ramos RT, Sá PH, Carneiro AR, Miranda F, Freire M, Renan W, Júnior AF, Santos AR, Pinto AC, Souza BM, Castro CP, Diniz CA, Rocha CS, Mariano DC, de Aguiar EL, Folador EL, Barbosa EG, Aburjaile FF, Gonçalves LA, Guimarães LC, Azevedo M, Agresti PC, Silva RF, Tiwari S, Almeida SS, Hassan SS, Pereira VB, Abreu VA, Pereira UP, Dorella FA, Carvalho AF, Pereira FL, Leal CA, Figueiredo HC, Silva A, Miyoshi A, Azevedo V