Bioinformatics Scientist: Microbiome & Transcriptomics Expert
Resume:
Igor Lobo, PhD
****.***@*****.***
Bioinformatician
linkedin.com/in/igor-lobo-phd-79b189134
SUMMARY
Experienced Bioinformatician with a Ph.D. in Genetics and Bioinformatics, specializing in multi-omics data analysis, NGS data analysis, and single cell multi-omics. Demonstrated expertise in bioinformatics, R, Python, pandas, and ML/AI. Proven ability to deliver impactful data analysis and data visualization solutions, leveraging great communication skills, collaboration, and a growth mindset to drive advancements that benefit humankind. Based in Hempstead and experienced in Hybrid model work environments, with a focus on maximizing impact. EXPERIENCE
Independent Bioinformatics Consultant AYRA Data & Discovery in Flow 10/2025 – present
● Founded and manage AYRA Data & Discovery in Flow, providing consulting services in genomics, transcriptomics, and microbiome data analysis for academic and research clients.
● Conduct bioinformatics analyses of microbiome datasets from Amazonian soil environments using 16S rRNA, ITS1, and shotgun metagenomics sequencing, enabling characterization of microbial diversity and functional potential across ecological conditions.
● Develop reproducible pipelines in R, Python, and Bash for microbiome profiling, taxonomic classification, diversity analysis, and data visualization.
● Perform differential gene expression analysis in Tambaqui (Colossoma macropomum) to investigate transcriptomic responses under different climate change scenarios, including temperature variation effects on early development.
● Apply statistical modeling and high-throughput sequencing analysis to support biological interpretation of environmental and organismal responses to ecological stressors.
● Maintain structured workflows, documentation, and version-controlled pipelines to ensure reproducibility and scalability of analyses Postdoctoral Researcher Icahn School of Medicine at Mount Sinai 10/2023 to 10/2025 Led genomic analyses of human antibody repertoires using high-throughput sequencing data and advanced bioinformatics pipelines. Characterized vaccine-induced immune responses by analyzing antibody repertoires from individuals vaccinated with XBB.1.5 mRNA and Novavax vaccines.
Performed statistical analysis and data mining on single-cell and bulk RNA-seq datasets to uncover transcriptional patterns and immune signatures.
Compared antibody responses to JYNNEOS vaccination and mpox infection through integrated single-cell repertoire and gene expression analysis.
Developed and maintained custom scripts in R, Python, and Bash for gene expression profiling, repertoire analysis, and genetic association studies.
Investigated the impact of immunoglobulin (IG) locus variants on antibody CDR3 composition by associating SNPs within IG loci with amino acid frequencies at specific CDR3 positions. Ph.D. in Genetics UFMG 10/2018 to 07/2023
Developed machine learning frameworks for reverse vaccinology, including: Natural language processing (NLP)-based predictor to extract vaccine-related information from biomedical literature, and; An ensemble model combining Random Forests, Support Vector Machines, and Autoencoders to identify vaccine candidates. Predicted parasite-derived vaccine candidates by integrating high-throughput sequencing data with advanced bioinformatics tools and genomic analysis.
Designed and implemented custom pipelines in R, Bioconductor, and Python for data mining, experimental planning, and reproducible analysis workflows.
Technical Support Embrapa 07/2017 to 07/2018
Analyzed the transcriptome of Tambaqui alevins, a key aquaculture species in the Amazon, to explore early developmental gene expression.
Uncovered molecular mechanisms underlying sexual differentiation in Tambaqui through transcriptomic and genomic analysis. Identified and validated candidate genes involved in sexual differentiation using bioinformatics tools and differential expression analysis. Managed and curated gene expression datasets, ensuring data integrity and facilitating downstream analysis. MSc. in Biotechnology Federal University of Amazonas (Universidade Federal do Amazonas)02/2014 to 07/2016 Analyzed transcriptome of Fusarium decemcellulare using high-throughput sequencing. Explored molecular aspects of plant-pathogen interaction with bioinformatics tools and statistical analysis. Contributed to disease control strategies by mining genomic data and designing experiments. Applied programming in R and Bash for gene expression. Undergraduate research in Molecular Biology Embrapa 08/2010 to 09/2013 Developed cloning vectors – Designed binary vectors for genetic transformation in fungi, enabling cost-effective gene knockouts. Validated transformation system – Implemented Agrobacterium-mediated transformation in Mycosphaerella fijiensis and Fusarium oxysporum, providing an alternative to traditional markers. Gene silencing via RNAi – Applied RNAi to silence the frp1 gene in F. oxysporum, advancing research on Panama disease in bananas. EDUCATION
Doctor of Philosophy - PhD in Genetics and Bioinformatics Universidade Federal de Minas Gerais 2018 to 2023 Focused on genetics and bioinformatics, with applications of machine learning to reverse vaccinology, predicting vaccine candidates based on parasite genomic data. Included extensive work in genomics, RNA Sequencing, and bioinformatics. SKILLS
Programming Problem-solving Database management
Analyzes large scale datasets Transcriptome assembling Bulk RNA-seq analysis (gene expression and differential transcript usage)
Independent work High-throughput sequencing Genomic analyses Statistical analysis Single-cell analysis (gene expression and large-scale characterization of B cell
receptor)
Communication
HONORS & AWARDS
2025 AAI Diversity Travel Award
Awarded by the American Association of Immunologists. CAPES - PrInt (Fellowship)
Exchange period: Aston University in 2022.
Untangling genomes through bioinformatics (Fellowship) Fellowship awarded by the Centro Brasileiro-Argentino de Biotecnologia in 2016. Bioinformatics in transcriptomic analysis (Fellowship) Fellowship awarded by the National Laboratory of Scientific Computation in 2014. Best oral presentation in 45th Brazilian Congress in Phytopathology Awarded by the Brazilian Society of Phytopathology PUBLICATIONS
Septic arthritis drives alveolar bone loss in mice through microbiota-dependent functional shifts. DAIANE BOFF, FELIPE HENRIQUE SILVA BAMBIRRA, CELSO MARTINS QUEIROZ-JUNIOR, THALES AUGUSTO ANESTINO, VIVAN LOUISE SOARES OLIVEIRA, LIVIA MARIA ALVES FERREIRA, IGOR LOBO, DIEGO LISBOA RIOS, MAURO MARTINS TEIXEIRA, TARCÍLIA APARECIDA SILVA, DANIELE GLÓRIA SOUZA, FLÁVIO ALMEIDA AMARAL. Microbial Pathogenesis, 2025. DOI: 10.1016/j.micpath.2025.108270.
Mapping of human monoclonal antibody responses to XBB.1.5 COVID-19 monovalent vaccines: a B cell analysis. RAIANNA F. FANTIN, HALLIE COHN, DEEPIKA JAISWAL, BAILEY BOZARTH, VISHAL RAO, ALESANDRO CIVLJAK, IGOR LOBO, JESSICA R. NARDULLI, KOMAL SRIVASTAVA, JEREMY YONG, ROBERT ANDREATA-SANTOS, KAITLYN BUSHFIELD, EDWARD LEE, GAGANDEEP SINGH, PVI STUDY GROUP, STEVEN KLEINSTEIN, JORDAN J. CLARK, VIVIANA SIMON, GORAN BAJIC, FLORIAN KRAMMER, CAMILA H. COELHO. Mapping of human monoclonal antibody responses to XBB.1.5 COVID-19 monovalent vaccines: a B cell analysis. The Lancet Microbe, 2025. DOI: 10.1016/j.lanmic.2025.101103. Transcriptomic Analysis of Tambaqui (Colossoma macropomum) Exposed to Trichlorfon-Induced Toxicity. Silva, Hallana Cristina Menezes da, Igor Kelvyn Cavalcante Lobo, André Gentil da Silva, Ana Lúcia Silva Gomes, Wallice Paxiúba Duncan, Juliana Costa Silva, Fabrício M. Lopes, Roberto Ferreira Artoni, and Daniele Aparecida Matoso. 2025. "Transcriptomic Analysis of Tambaqui
(Colossoma macropomum) Exposed to Trichlorfon-Induced Toxicity" Animals 15, no. 12: 1807. https://doi.org/10.3390/ani15121807 Organism-specific training improves performance of linear B-cell epitope prediction. ASHFORD, JODIE; REIS-CUNHA, JOÃO; LOBO, IGOR; LOBO, FRANCISCO; CAMPELO, FELIPE. Organism-specific training improves performance of linear B-cell epitope prediction. Bioinformatics, btab536, 2021. Transcriptome of tambaqui Colossoma macropomum during gonad differentiation: Different molecular signals leading to sex identity. LOBO, IGOR KELVYN CAVALCANTE; NASCIMENTO, ÁQUILA RODRIGUES DO; YAMAGISHI, MICHEL EDUARDO BELEZA ; GUIGUEN, YANN ; SILVA, GILVAN FERREIRA DA ; SEVERAC, DANY ; AMARAL, ALDESSANDRO DA COSTA ; REIS, VANESSA RIBEIRO ; ALMEIDA, FERNANDA LOUREIRO DE . Transcriptome of tambaqui Colossoma macropomum during gonad differentiation: Different molecular signals leading to sex identity. GENOMICS, v. 112, p. 2478-2488, 2020. Morpho-Anatomical and Molecular Characterization of the Oversprouting Symptoms Caused by Fusarium decemcellulare in Guarana Plants (Paullinia cupana var. sorbilis).
DE QUEIROZ, CLAUDIA AFRAS ; DA SILVA MATOS, KEDMA; LOBO, IGOR KELVYN CAVALCANTE ; DE SOUSA, SANDRA BARBOSA ; MUNIZ, CELLI RODRIGUES ; BELEZA YAMAGISHI, MICHEL E. ; ZOCOLO, GUILHERME JULIÃO ; HANADA, ROGÉRIO EIJI ; GASPAROTTO, LUADIR ; SOUSA, NELCIMAR REIS ; DE ANDRADE, EDMAR VAZ ; CORDEIRO, ISABELLE BEZERRA ; MELO, ANDERSON ADRIANO MARTINS ; DA SILVA, GILVAN FERREIRA . Morpho-Anatomical and Molecular Characterization of the Oversprouting Symptoms Caused by Fusarium decemcellulare in Guarana Plants (Paullinia cupana var. sorbilis). Tropical Plant Biology, v. 13, p. 274-286, 2020.
REVISION FOR SCIENTIFIC JOURNALS
Reviewer for Manuscripts: Frontiers in Bioinformatics.
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