📄 Curriculum Vitae
[INVESTIGATOR PROFILE]

Allysson Allan de Farias, PhD

Visiting Professor & HPC Manager Postgraduate Program in Translational Medicine (PPGMTM) • Universidade Federal do Ceará (UFC) Senior Bioinformatician & Research Collaborator • Universidade Estadual da Paraíba (UEPB)

I am a geneticist and bioinformatician investigating human population demography, ancient DNA (aDNA) taphonomic degradation, and the medical genomics of admixed populations. With a doctorate in Genetics from the University of São Paulo (USP) and a master's in Archaeology from the Federal University of Pernambuco (UFPE), my research examines bone diagenesis and post-mortem cytosine deamination kinetics, models ancestral mutation ages in Northeast Brazilian isolates, and architects production Nextflow and Slurm pipelines on national supercomputing clusters.

🔬 Research Programs 📖 Verified Publications 🎓 Google Scholar
[CORE RESEARCH THEMES]

Research Programs & Methodologies

Focused lines of inquiry across ancient DNA authentication, medical genomics of admixed cohorts, and distributed computational pipelines.

§ 01 Ancient DNA

Paleogenomic Authentication, Damage Kinetics & Evolutionary Demography

End-to-end paleogenomic pipelines for recovering authentic genomic reads from archaeological remains (petrous bone, tooth dentin, and sediment cores), grounded in our experimental diagenesis work (JAS: Reports 2026; protocols.io 2026). In ultraclean room environments, taphonomic degradation is assessed: short fragment distributions (35–70 bp) driven by depurination, and terminal single-stranded 5′ cytosine deamination ($C \to U \to T$) with complementary 3′ $G \to A$ transitions. Bayesian damage rate estimation (mapDamage 2.0) and post-mortem filtering (PMDtools) authenticate endogenous ancient molecules against modern contamination, enabling rigorous downstream $f$-statistics ($f_3, f_4$), $f_4$-ratio introgression modeling, and multi-source qpAdm admixture graphs.

Bone Diagenesis mapDamage 2.0 PMDtools UDG-half Prep qpAdm / qpGraph Archaic Introgression
§ 02 Population Genomics

Tri-Hybrid Admixture Dynamics, Local Chromosome Painting & Autozygosity

High-resolution deconvolution of Brazilian tri-hybrid demographic architectures derived from Native American, Western/Central African, and European ancestral sources. Chromosome painting algorithms (RFMix v2, ChromoPainter) resolve phased ancestral tracts along homologous chromosomes. In isolated Northeast Brazilian populations with historical endogamy (Farias et al., Scientific Reports 2018, 2020), scanning for extended Runs of Homozygosity (ROH / autozygosity) uncovers founder pathogenic mutations in genes such as KLC2, IMPA1, MED25, and WNT7A, while cross-ancestry calibration of Polygenic Risk Scores (PRS) overcomes Eurocentric predictive biases in clinical cohorts (J Mol Diagn 2024).

RFMix v2 Chromosome Painting Autozygosity / ROH Consanguinity Isolates Multi-Ancestry PRS Founder Mutations
§ 03 HPC Architecture

Distributed Supercomputing, Slurm & Nextflow DSL2 Orchestration

Production-grade computational frameworks deployed across national and international supercomputing centers (Santos Dumont LNCC, Carlos Chagas Fiocruz, Sun USP HUG-CELL, and Rocket Tartu / UFC). Pipelines orchestrate raw sequence ingestion, base quality score recalibration (BQSR), reference mapping (BWA-MEM2, Bowtie2), and joint variant calling (GATK4, DeepVariant). Encapsulated via Nextflow DSL2 with Singularity/Apptainer containers, workflows execute deterministically with automated checkpointing and scale into cloud biobank matrix analytics using Hail on Apache Spark and AWS HealthOmics.

Slurm Workload Manager Nextflow DSL2 Singularity Containers Santos Dumont (LNCC) Hail on Spark AWS HealthOmics
§ 04 Metagenomics

Metagenomic Taxonomic Deconvolution, Resistome Profiling & Pathogen Tracking

High-throughput metagenomic surveillance spanning environmental sediment microbiomes and urban wastewater treatment plants (Braz J Microbiol 2026) to clinical pathogen surveillance (Anal Chem 2024; Pediatr Res 2025). Features automated host-depletion, exact $k$-mer taxonomic assignment with Lowest Common Ancestor (LCA) resolution (Kraken2, Bracken), antimicrobial resistance (AMR) resistome profiling against the Comprehensive Antibiotic Resistance Database (CARD), and time-scaled coalescent phylodynamic tracking (Nextstrain) informing epidemiological surveillance.

Kraken2 / Bracken Wastewater Genomics AMR Resistome CARD / RGI Nextstrain Epidemiological Surveillance
[VERIFIED SCIENTIFIC RECORD]

Selected Publications & Theses

Verified research articles and dissertations indexed on Google Scholar, ORCID (0000-0002-5322-1785), and NCBI PubMed.

Journal Article • Nature Publishing Group

Cord blood cytokines/chemokines linked to delays in toddlers exposed to SARS-CoV-2 prenatally

Kehdi, R. C., Silva, M. F. S., Cavalcante, L. R. L., Fiorenza, N. G., Viana, M., Leite, I. B., Silva, B. R. S., Assis, D. F., Cortez, P. C., Bezerra, D. L., Motta, P. C., Marques, J. A. L., Chaves Filho, A. J. M., Correia, É., Farias, A. A., Miyajima, F., Teixeira, A. L., Thomason, M. E., Carvalho, F. H. C., & Macedo, D. S.

Pediatric Research, 98(5), 1817–1826 (2025) • DOI: 10.1038/s41390-025-04192-w • PMID: 40500279

[ACADEMIC & RESEARCH APPOINTMENTS]

Professional Appointments

Chronological record of academic faculty appointments, research positions, and bioinformatic leadership roles.

2024 – Present

Visiting Professor & HPC Manager

Universidade Federal do Ceará (UFC) • Translational Medicine Program (PPGMTM)

Directing high-performance computing operations, advising postgraduate cohorts, and developing automated pipelines for clinical genomic discovery.

2023 – 2024

Bioinformatics Manager

Fundação Oswaldo Cruz (Fiocruz-CE)

Supervised multidisciplinary bioinformatician and engineer teams developing distributed data pipelines and pathogen surveillance infrastructures for public health monitoring.

2022 – 2023

Principal AI Lab & Analytics Specialist

Farmácias Pague Menos (Retail Healthcare)

Led predictive analytics and machine learning initiatives for large-scale epidemiological and retail healthcare systems.

2020 – 2021

Postdoctoral Researcher

Università degli Studi di Padova (Italy)

Investigated cross-ancestry transferability of Polygenic Risk Scores (PRS) in complex admixed population cohorts.

2014 – Present

Senior Bioinformatician & Research Collaborator

Universidade Estadual da Paraíba (UEPB)

Handling population genomic datasets, investigating rare autosomal recessive diseases in endogamous Northeast Brazilian isolates, and teaching computational tools (R, Python, Bash).

Industry

Senior Healthcare Data Scientist

Hospital Israelita Albert Einstein & Hapvida Saúde

Engineered clinical analytics systems and predictive models supporting hospital decision-making and patient outcome optimization.

[ACADEMIC DISCOVERY]

Connect & Collaborate

Explore published manuscripts, open-source repositories, and official academic records across verified international indexing databases:

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🎓 Google Scholar 🆔 ORCID iD 📜 Lattes CV 💻 GitHub 💼 LinkedIn 🔬 ResearchGate 🌐 Web of Science