CV

Education

• D.Sc., Animal Science and Pastures, University of São Paulo - Piracicaba.
  • Dissertation: “Multi-omic data integration for the study of production, carcass and meat quality traits in Nellore cattle”.
  • Advisor: Dr. Luiz Lehmann Coutinho.
• M.Sc., Animal Biocience, University of São Paulo-Pirassununga
  • Thesis: “Analysis in serum metabolomic associated with feed efficiency in Nellore”.
  • Advisor: Dr. Heidge Fukumasu.
• B.S., Animal Science, University of São Paulo-Pirassununga
  • Advisor: Dr. Heidge Fukumasu.

Work experience

• August 2022- Now : Postdoctoral fellow at University of Alberta
  • Faculty of Agricultural, Life & Environmental Sciences
  • Supervisor: Edward Bork, Carolyn Fitzsimmons
  • Postodoc in Data Science and Precision Livestock Farming
• September 2021- August 2022: Postdoctoral fellow at University of São Paulo
  • Department of Medicine Veterinary, FZEA/USP
  • Supervisor: Heidge Fukumasu
  • Postodoc in Machine-learning applied to Metagenomics
• August 2017 - September 2021: Graduate Research Assistant (D.Sc.)
  • Department of Animal Science, ESALQ/USP
  • Advisor: Luiz Lehmann Coutinho
  • Grant number: 88882.328657/2019-01 (CAPES)
  • My P.h.D research has focused on Multi-omics Data integration methods applied to meat quality in Nellore cattle.
• August 2019 - February 2020: Exchange Visitor
  • Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg,VA.
  • Supervisor: Gota Morota
  • Grant number: 88887.367967/2019-00 (CAPES)
  • During the six-months internship I was training on machine-learning approaches applied to data omics integration.
• Ouctober 2016- April 2017: Exchange Visitor
  • School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta,GA.
  • Supervisor: Mark Styczynski
  • Grant number: 16/16214-8 (FAPESP)
  • During the six-months internship I was training on preprocessing, univarite and multivariate analysis for metabolomics.
• Ouctober 2014- June 2017: Graduate Research Assistant (M.Sc.)
  • Department of Medicine Veterinary, FZEA/USP
  • Advisor: Heidge Fukumasu
  • Grant number: 15/01059-4 (FAPESP)
  • My research was focused to identify potential biomarkers associated with feed efficiency as well as to understand the molecular process that explains feed efficiency variation.
• August 2013- June 2014: Technical Assistant
  • CRV Lagoa Ltda, Sertãozinho, São Paulo
  • Dairy Cattle Animal Breeding Program
  • At CRV Lagoa he worked with the database of animal breeding program for dairy cattle, he also supported dairy cattle mating via CRV ’s mating program.
• December 2012- June 2013: Undergraduate Research Assistant
  • Department of Basic Science, FZEA/USP
  • Grant number: 12/17153-1 (FAPESP)
  • Advisor: Heidge Fukumasu
  • Project:”Standardization of Genome Wide Association Study (GWAS) based on DNA pooling and allelotyping in high density arrays in Nellore”
  • The aim of this work is standardize an experimental model for phase one GWAS based on DNA pooling from animals with high and low efficiency for age at first calving simultaneously with higher body weight gain of calves.
• June 2011- June 2012: Undergraduate Research Assistant
  • Department of Basic Science, FZEA/USP
  • Grant: CNPq
  • Advisor: José Bento Sterman Ferraz
  • Project:”Genetic and Phenotypic correlations between rump eye area and backfat thickness mesuared in different anatomics points of Longissimus Dorsi of Nellore cattle”

Skills

• Quantitative Skills

  • Transcriptome Analysis
    • RNA-sequencing: DEseq2, NOISeq, EdgeR, LIMMA
    • Co-expression network analysis: Weighted Gene Coexpression Network Analysis (WGCNA), Cytoscape
  • Metagenomics Analysis
    • Processing and Phylogenetics: Fastqc. Multiqc, Figaro, HTStream, DADA2, Phyloseq, Vegan
    • Statistical Analysis: Phyloseq, DEseq2, EdgeR
  • Metabolomics Analysis
    • Preprocessing: Progenesis QI Software, XCMS
    • Statistical Analysis: MetaboAnalyst
    • Putative Identification: mummichog
  • Statistics
    • R

• Computational Skills

  • Operating Systems: LINUX, Windows
    • R skills: LATEX, ggplot2, Tidyr, dplyr, stringr, purrr, tibble.
    • Photoshop and profissional slides.

Publications

Genome-wide association with residual body weight gain in Bos indicus cattle

M.H.A. Santana, R.C. Gomes, Y.T. Utsunomiya, H.H.R. Neves, F.J. Novais, M.N. Bonin, H. Fukumasu, J.F. Garcia, P.A. Alexandre, G.A. Oliveira Junior, L.L. Coutinho (2015) Genome-wide association with residual body weight gain in Bos indicus cattle. Genetics and Molecular Research Volume: 14 Issue: 2 Pages: 5229-5233

Visual body-scores selection and its influence on body size and ultrasound carcass traits in Nellore cattle

M. N. Bonin J. B. S. Ferraz V. B. Pedrosa S. L. Silva R. C. Gomes D. C. Cucco M. H. A. Santana J. H. A. Campos V. N. Barbosa F. S. F. Castro F. J. Novais E. C. M. Oliveira (2015).Visual body-scores selection and its influence on body size and ultrasound carcass traits in Nellore cattle. Journal of Animal Science, Volume 93, Issue 12, December 2015, Pages 5597–5606.

Circulating leptin and its muscle gene expression in Nellore cattle with divergent feed efficiency

L.F.M. Mota, C.M. Bonafé, P.A. Alexandre, M.H. Santana, F.J. Novais , E. Toriyama, A.V. Pires, S.L. Silva, P.R. Leme, J.B.S. Ferraz and H. Fukumasu(2017)Circulating leptin and its muscle gene expression in Nellore cattle with divergent feed efficiency.Journal of Animal Science and Biotechnology Volume: 8 Pages:71

Identification of a metabolomic signature associated with feed efficiency in beef cattle

F.J. Novais , P.R.L. Pires, P.A. Alexandre, R.A. Dromms, A.H. Iglesias, J.B.S. Ferraz, M.P. Styczynski and H. Fukumasu(2017),Identification of a metabolomic signature associated with feed efficiency in beef cattle.BMC Genomics Volume: 20 Issue: 1 Pages: 8

Identification of selection signatures involved in performance traits in a paternal broiler line

O.A.C. Almeida, G.C.M. Moreira, F.M. Rezende, C. Boschiero, J. O. Peixoto, A.M.G. Ibelli, M.C. Ledur, F.J. Novais and L.L Coutinho (2019) Identification of selection signatures involved in performance traits in a paternal broiler line. BMC Genomics Volume: 20 Issue: 1 Pages: 449

Genetic parameters associated with meat quality of Nellore cattle at different anatomical points of longissimus: Brazilian standards

Marina de Nadai Bonin,Victor Breno Pedrosa, Saulo da Luz e Silva, Lutz Bünger, Dave Ross, Rodrigo da Costa Gomes, Miguel Henrique de Almeida Santana, Diego de Córdova Cucco, Fernanda Marcondes de Rezende, Luís Carlos Vinhas Ítavo, Francisco José de Novais, Marília Williani Filgueira Pereira, Elisângela Chicaroni de Mattos Oliveira, José Bento Sterman Ferraz (2021) Genetic parameters associated with meat quality of Nellore cattle at different anatomical points of longissimus: Brazilian standards. Meat Science Volume: 171 Pages: 108281

Metabolomic signature of spermatozoa established during holding time is responsible for differences in boar sperm freezability

Mariana A Torres, Ana Carolina Pedrosa, Francisco José de Novais, Diego V Alkmin, Bruce R Cooper, George S Yasui, Heidge Fukumasu, Zoltan Machaty, André F C de Andrade (2021) Metabolomic signature of spermatozoa established during holding time is responsible for differences in boar sperm freezability. Biology of Reproduction, ioab200

Vaginal Microbiota Diversity in Response to Lipopolysaccharide in Gilts Housed Under Three Housing Systems

Alves Luana, Francisco José de Novais, da Silva Arthur Nery, Araujo Michelle Silva, Bernardino Thiago, Osowski Germana Vizzotto, Zanella Ricardo, Lee Settles Matthew, Holmes Mark A., Fukumasu Heidge, Ruiz Vera Letticie de Azevedo, Zanella Adroaldo José (2022) Vaginal Microbiota Diversity in Response to Lipopolysaccharide in Gilts Housed Under Three Housing Systems. Frontiers in Genetics, v. 13

Multi-omic data integration for the study of production, carcass, and meat quality traits in Nellore cattle

Francisco José de Novais, Haipeng Yu, Aline Silva Mello Cesar, Mehdi Momen, Mirele Poleti, Bruna Petry, Gerson Mourão, Luciana Regitano, Gora Morota, Luiz Lehmann Coutinho (2022) Multi-omic data integration for the study of production, carcass, and meat quality traits in Nellore cattle. Frontiers in Genetics, v. 13

Predicting the shear value and intramuscular fat in meat from Nellore cattle using Vis-NIR spectroscopy

M.N. Bonin, S.L. Silva, L. Bünger, D. Ross, G.L.D. Feijó and R.C. Gomes and F.P. Rennó and M.H.A. Santana, F.M. Rezende, L.C.V. Ítavo, F.J. Novais, L.M.A. Surita, M.N. Bonin, M.H.F Pereira and J.B.S. Ferraz(2020) Predicting the shear value and intramuscular fat in meat from Nellore cattle using Vis-NIR spectroscopy. Meat Science Pages: 108077

Talks

Teaching