Felipe da Veiga Leprevost

Biological Data Science & Visualization
Content

Peer-Reviewed Publications

You can also find me on Google Scholar.
My ORCID ID is 0000-0002-8228-5374.

Published
  • Jiang W, Wen B, Li K, Zeng WF, da Veiga Leprevost F, Moon J, Petyuk VA, Edwards NJ, Liu T, Nesvizhskii AI, Zhang B. Deep learning-derived evaluation metrics enable effective benchmarking of computational tools for phosphopeptide identification. Mol Cell Proteomics. 2021 Nov 1:100171.

  • Cao L, Huang C, Cui Zhou D, et al. Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell. 2021;184(19):5031-5052.e26.

  • Weber SR, Zhao Y, Ma J, da Veiga Leprevost F et al. A Validated Analysis Pipeline for Mass Spectrometry-Based Vitreous Proteomics: Insights Into Proliferative Diabetic Retinopathy, Research Square, 2021

  • Satpathy S, Krug K, Jean Beltran PM, et al. A proteogenomic portrait of lung squamous cell carcinoma. Cell. 2021;184(16):4348-4371.e40.

  • Goudsmit C, da Veiga Leprevost F, Basrur V, Peters L, Nesvizhskii A, Walline H. Differences in Extracellular Vesicle Protein Cargo Are Dependent on Head and Neck Squamous Cell Carcinoma Cell of Origin and Human Papillomavirus Status. Cancers. 2021; 13(15):3714.

  • Weber SR, Zhao Y, Gates C, et al. Proteomic Analyses of Vitreous in Proliferative Diabetic Retinopathy: Prior Studies and Future Outlook. J Clin Med. 2021;10(11):2309. Published 2021 May 25.

  • Huang C, Chen L, Savage SR, et al. Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma. Cancer Cell. 2021;39(3):361-379.e16.

  • Geiszler DJ, Kong AT, Avtonomov DM, Yu F, da Veiga Leprevost F, Nesvizhskii AI. PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results. Mol Cell Proteomics. 2020;20:100018.

  • Petralia F, Tignor N, Reva B, et al. Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer. Cell. 2020;183(7):1962-1985.e31.

  • Hoang SM, Kaminski N, Bhargava R, et al. Regulation of ALT-associated homology-directed repair by polyADP-ribosylation. Nat Struct Mol Biol. 2020;27(12):1152-1164.

  • da Veiga Leprevost F, Haynes SE, Avtonomov DM, et al. Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods. 2020;17(9):869-870.

  • Gillette MA, Satpathy S, Cao S, et al. Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma. Cell. 2020;182(1):200-225.e35.

  • Djomehri SI, Gonzalez ME, da Veiga Leprevost F, et al. Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors. Nat Commun. 2020;11(1):1723. Published 2020 Apr 7.

  • Chang HY, Kong AT, da Veiga Leprevost F, Avtonomov DM, Haynes SE, Nesvizhskii AI. Crystal-C: A Computational Tool for Refinement of Open Search Results. J Proteome Res. 2020;19(6):2511-2515.

  • Cho KC, Clark DJ, Schnaubelt M, et al. Deep Proteomics Using Two Dimensional Data Independent Acquisition Mass Spectrometry. Anal Chem. 2020;92(6):4217-4225.

  • Clark DJ, Dhanasekaran SM, Petralia F, et al. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma Cell. 2019;179(4):964-983.e31.

  • Wippel HH, Malgarin JS, Inoue AH, et al. Unveiling the partners of the DRBD2-mRNP complex, an RBP in Trypanosoma cruzi and ortholog to the yeast SR-protein Gbp2. BMC Microbiol. 2019;19(1):128. Published 2019 Jun 11.

  • Gruening B, Sallou O, Moreno P, et al. Recommendations for the packaging and containerizing of bioinformatics software. F1000Res. 2018;7:ISCB Comm J-742. Published 2018 Jun 14.

  • Hawkins AG, Basrur V, da Veiga Leprevost F, et al. The Ewing Sarcoma Secretome and Its Response to Activation of Wnt/beta-catenin Signaling. Mol Cell Proteomics. 2018;17(5):901-912.

  • da Veiga Leprevost F, Grüning BA, Alves Aflitos S, et al. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017;33(16):2580-2582.

  • Trevisan-Silva D, Bednaski AV, Fischer JSG, et al. A multi-protease, multi-dissociation, bottom-up-to-top-down proteomic view of the Loxosceles intermedia venom. Sci Data. 2017;4:170090. Published 2017 Jul 11.

  • Kong AT, da Veiga Leprevost F, Avtonomov DM, Mellacheruvu D, Nesvizhskii AI. MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics. Nat Methods. 2017;14(5):513-520.

  • Perez-Riverol Y, Bai M, da Veiga Leprevost F, et al. Discovering and linking public omics data sets using the Omics Discovery Index. Nat Biotechnol. 2017;35(5):406-409.

  • Santos RM, Nogueira FC, Brasil AA, et al. Quantitative proteomic analysis of the Saccharomyces cerevisiae industrial strains CAT-1 and PE-2. J Proteomics. 2017;151:114-121.

  • Perez-Riverol Y, Gatto L, Wang R, et al. Ten Simple Rules for Taking Advantage of Git and GitHub PLoS Comput Biol. 2016;12(7):e1004947. Published 2016 Jul 14.

  • Borges MH, Figueiredo SG, da Veiga Leprevost F, et al. Venomous extract protein profile of Brazilian tarantula Grammostola iheringi: searching for potential biotechnological applications. J Proteomics. 2016;136:35-47.

  • Carvalho PC, Lima DB, da Veiga Leprevost F, et al. Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0. Nat Protoc. 2016;11(1):102-117.

  • Brunoro GV, Caminha MA, Ferreira AT, et al. Reevaluating the Trypanosoma cruzi proteomic map: The shotgun description of bloodstream trypomastigotes. J Proteomics. 2015;115:58-65.

  • da Veiga Leprevost F, Valente RH, Lima DB, et al. PepExplorer: a similarity-driven tool for analyzing de novo sequencing results. Mol Cell Proteomics. 2014;13(9):2480-2489.

  • da Veiga Leprevost F, Barbosa VC, Francisco EL, Perez-Riverol Y, Carvalho PC. On best practices in the development of bioinformatics software. Front Genet. 2014;5:199. Published 2014 Jul 2.

  • da Veiga Leprevost F. 2014. Bio::DB::NextProt: A Perl Module for neXtProt Database Information Retrieval. PeerJ PrePrints 2:e372v1

  • Fischer Jde S, Canedo NH, Goncalves KM, et al. Proteome analysis of formalin-fixed paraffin-embedded tissues from a primary gastric melanoma and its meningeal metastasis: a case report. Curr Top Med Chem. 2014;14(3):382-387.

  • da Veiga Leprevost F, Lima DB, Crestani J, et al. Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics. J Proteomics. 2013;89:179-182.

  • Borges D, Perez-Riverol Y, Nogueira FC, et al. Effectively addressing complex proteomic search spaces with peptide spectrum matching. Bioinformatics. 2013;29(10):1343-1344.

Book Chapters

Invited Talks

Conference Presentations

  • The role of Perl in the Brazilian startup ecosystem.
    Talk - YAPC::Brazil 2013 – 10|2013 – Curitiba, Brazil.

  • BioCoders: Standards and best practices for bioinformatics.
    Talk - YAPC::Brazil 2013 – 10|2013 – Curitiba, Brazil.

  • PepExplorer: Organizing and Filtering of de novo Results.
    Talk - HavanaBioinfo 2012 – 06|2012 – Havana, Cuba.

  • Big (Bio) Data.
    Talk - YAPC::Brazil 2012 – 10|2012 – São Paulo, Brazil.

  • PepExplorer: Organizing and Filtering of de novo Results.
    Talk - Fiocruz Academic Week – 02|2012 – Curitiba, Brazil.

Contributions to Scientific Software

  • Geiszler DJ, Kong AT, Avtonomov DM, Yu F, da Veiga Leprevost, Nesvizhskii AI. 2020: PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results, available on GitHub.

  • da Veiga Leprevost, Haynes SE, Avtonomov DM, Chang HY, Shanmugam AK, Mellacheruvu D, Kong AT, Nesvizhskii AI. 2020: Philosopher: a versatile toolkit for shotgun proteomics data analysis, available on GitHub.

  • Chang HY, Kong AT, da Veiga LeprevostAvtonomov DM, Haynes SE, Nesvizhskii AI. 2020: Crystal-C: A Computational Tool for Refinement of Open Search Results, available on GitHub.

  • Kong AT, da Veiga Leprevost, Avtonomov DM, Mellacheruvu D, Nesvizhskii AI. 2017: MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics, available on BioContainers.

  • da Veiga Leprevost, Grüning BA, Alves Aflitos S, et al. 2017: BioContainers: an open-source and community-driven framework for software standardization, available on BioContainers.

  • Carvalho PC, Lima DB, da Veiga Leprevost, et al. 2016: PatternLab for proteomics: an integrated computational environment for analyzing shotgun proteomic data, available on PatternLab.

  • da Veiga Leprevost, Valente RH, Lima DB, et al. 2014: PepExplorer: a similarity-driven tool for analyzing de novo sequencing results, available on PatternLab.

Contributions to CPAN

  • da Veiga Leprevost 2016: Bio::KEGG::API: A Perl interface to KEGG API, available on CPAN.

  • da Veiga Leprevost 2015: PepXML::Parser: A Perl parser for the pep.xml file format, available on CPAN.

  • da Veiga Leprevost 2014: MzML::Parser: A Perl parser for the mzML data format, available on CPAN.

  • da Veiga Leprevost 2014: Bio::Tools::ProteinogenicAA: An object list of proteinogenic amino acids, available on CPAN.

  • da Veiga Leprevost 2014: Lingua::Sindarin::Dictionary: A Dictionary for the Sindarin language, available on CPAN.

  • da Veiga Leprevost 2014: Bio::DB::NextProt: An Object interface to the neXtProt REST API, available on CPAN.

  • da Veiga Leprevost 2014: Journal::ImpactFactor: A list of updated scientific journal impact factor, available on CPAN.

  • da Veiga Leprevost 2014: MS2::Parser: A generic parser for the MS2 file format, available on CPAN.

  • da Veiga Leprevost 2014: EveOnline::Api: A Perl version of the Eve Online API system, available on CPAN.

  • da Veiga Leprevost 2014: Bio::Tools::Alignment::Overview: Just another represetation for biological sequence alignment, available on CPAN.

  • da Veiga Leprevost 2013: Math::SparseMatrix::Operations: Mathematical operations with matrices, available on CPAN.

  • da Veiga Leprevost 2013: AI::NeuralNet::Hopfield: A simple Hopfiled Network Implementation, available on CPAN.