Dany Domínguez Pérez
PhD · Marine Bioinformatics & OMICs Scientist · PagBiOmicS Founder
Marine Bioinformatics
Venomics
OMICs
Bioactive Peptides
Toxinology
PagBiOmicS Founder
455
Google Scholar Citations
15
h-index
18
i10-index
22+
Journal Articles
2
Book Chapters
23
Conference Events
About
Research Profile
Highly motivated researcher specializing in high-throughput biodiscovery of bioactive peptides with ecological, biomedical, and industrial applications — including toxin-like, antimicrobial, antitumor, antiparasitic, and antiviral peptides. Expert in proteotranscriptomics, venomics, marine ecotoxicology, and OMICs-based biomarker identification across non-model organisms.
From February 2024 to January 2026, served as Research Fellow at Stazione Zoologica Anton Dohrn (Naples, Italy), characterizing the venomous repertoire of deep-sea cnidarians from Mediterranean Italian coasts via proteotranscriptomics. Since February 2026, works independently as researcher, bioinformatics consultant, and B2B specialist in life sciences through PagBiOmicS.
Career
Professional Experience
Founder & Principal Bioinformatics Consultant
PagBiOmicS · Independent · Porto, Portugal
- Independent B2B consulting in bioinformatics, OMICs analysis, and academic guidance for researchers, biotech companies, and startups.
- Developing d'BiYOK Lab: BYOK AI-powered tools for researchers (JobApp AI Assistant and pipeline).
Research Fellow (Investigador)
Stazione Zoologica Anton Dohrn · Naples, Italy
- CRIMAC_DEEPVEN project: characterized deep-sea Anthozoa venom diversity via proteotranscriptomics (Italian MUR funding).
- Applied RNAseq and proteomics pipelines to characterize the venomous repertoire of mesophotic-zone cnidarians.
- Oral presentation at EUVEN 2024: "Toxin Repertoire of the False Black Coral Savalia savaglia from Mediterranean Mesophotic Zone Revealed by RNAseq Approach."
Assistant Researcher & Co-Manager
CIIMAR – Universidade do Porto · Portugal
- Led research on MOREBIVALVES project (FCT-funded): differential gene/protein expression in contaminated bivalves using toxicological and proteogenomic approaches.
- Managed laboratory platforms, co-supervised students, and contributed to grant reporting.
Research Assistant (Molecular Biology & Proteomics Platform)
CIIMAR – Universidade do Porto · EMBRC-PT · Portugal
- Coordinated the Molecular Biology and Proteomics platform within the European Marine Biological Resource Centre (EMBRC-PT).
Independent B2B Consulting in Biotech/Life Sciences
Iberian Market · Portugal & Spain
- Managed B2B accounts, client relations, and technical presentations across the Iberian market in the life sciences sector.
University Lecturer — Animal Physiology & Biological Fieldwork
Universidad Central Marta Abreu de Las Villas · Cuba
- Taught Animal Physiology and Biophysics at undergraduate level; coordinated Biological Fieldwork practical courses.
Training
Education & Training
PhD in Biology
Universidade do Porto, Faculdade de Ciências · Portugal
- FCT excellence fellowship (SFRH/BD/80592/2011). Thesis: "Proteomics and Transcriptomics of Venomous Animals". Approved.
Degree in Biological Sciences (BSc)
Universidad de La Habana · Cuba
- Thesis: "Toxicological and Pharmacological Properties of a Low Molecular Weight Fraction from Zoanthus sociatus (Cnidaria) assessed in OF-1 Mice." Grade: 4.41/5.
Postgraduate Certificate in Teaching & Learning in Higher Education
Universidad Central Marta Abreu de Las Villas · Cuba
- Grade: 4.5/5. English B2 — CAELTIC (UCLV, 2010).
Selected Postgraduate Courses
Single-Cell Technology
The Single-Cell World, Portugal · 2023
Bulk RNA-Seq Data Analysis
Udemy · 2023
Gene Expression Analysis in R
Udemy · 2023
Biopython for Bioinformatics
Udemy · 2023
R for Biological Sciences (Statistics)
CIIMAR / Universidade do Porto · 2019–2020
Proteomics Courses
CIIMAR / IBV Valencia · 2014–2015
Funding
Projects & Grants
CRIMAC_DEEPVEN — Venomous Repertoire of Deep-Sea Cnidarians from Mediterranean Italian Coasts
Stazione Zoologica Anton Dohrn · Italian MUR
- Research Fellow. Applied proteotranscriptomics and bioinformatics to characterize venom repertoire of deep-sea Anthozoa from Mediterranean Sea.
MOREBIVALVES — Molecular Strategies for Depuration of Commercial Bivalves
CIIMAR / FCT · PTDC/ASP-PES/31762/2017
- Investigator. Differential gene/protein expression analysis in bivalves contaminated with diarrhetic shellfish toxins.
EMBRC-PT — European Marine Biological Resource Centre
CIIMAR / European Commission · EMBRC-1-2017-023
- Research Technical Fellow. Coordinated Molecular Biology and Proteomics platform.
PhD Fellowship — Genomics of Venomous Animals from Cuba
FCT · SFRH/BD/80592/2011
Evolutionary Genomic Analyses of Toxic Cyanobacteria
FCT · Provided by PTCRIS: 104983
- Investigator. Molecular mechanisms for detoxification of cyanotoxins across metazoan species.
Output
Peer-Reviewed Journal Articles
22 peer-reviewed articles · Sorted by year (most recent first)
Open Access
Open Access1 citation
Open Access13 citationsCo-first author
Open Access64 citations
Open Access10 citations
Open Access17 citations
Open Access22 citations
Open Access9 citations
Open Access21 citations
Open Access30 citations
Open Access17 citations
Open Access26 citations
Open Access37 citationsCover Story · Special IssueFlagship Paper
Microcystin-LR Detected in a Low Molecular Weight Fraction from a Crude Extract of Zoanthus sociatus
Open Access8 citations
Open Access15 citations
Output
Book Chapters
Omics Advances in the Study of Zooplankton: Big Data for Small Drifting Organisms
In: Zooplankton Ecology, CRC Press/Taylor & Francis, pp. 264–277
- Matos A, Ledoux JB, Domínguez Pérez D, Almeida D, Antunes A. 8 citations
Detección de Puntos e Intervalos de Interés en la Señal ECG de Ratones
In: V Latin American Congress on Biomedical Engineering CLAIB 2011. Springer, pp. 1170–1173
- Kairuz HA, Mendoza MA, Domínguez D · DOI: 10.1007/978-3-642-21198-0_297
Preprint: SeqLengthPlot v1 (bioRxiv, 2024) — doi: 10.1101/2024.06.07.597948 — subsequently published in Bioinformatics Advances.
Presentations
Conference Contributions
Oral Presentations
Toxin Repertoire of the False Black Coral Savalia savaglia from Mediterranean Mesophotic Zone Revealed by RNAseq Approach
2nd International Congress EUVEN · Darwin-Dohrn Museum · Naples, Italy
Avances en el estudio de la genómica de animales venenosos de Cuba
CYTED BIOTOX — IBV, Valencia, Spain
Selected Posters
Biosynthesis of antibiotics: a highlighted pathway in the proteome of Bunodactis verrucosa
FAPRONATURA, Cuba · 2018
Harderian gland transcriptomics: toxin expression in three Cuban snakes
XII Pan American IST, Belgium · 2016
First evidence of Microcystin LR (MC-LR) in Zoanthus sociatus
10th ICTC, USA · 2016
The Queen Conch (Lobatus gigas) Proteome
Proteomic Forum 2019, Potsdam, Germany
Medusozoa in Portugal: DNA-based tools for early forecasting of mass occurrences
XX SIEBM, Braga, Portugal · 2019
Transcriptomic profile of Cerastoderma edule exposed to diarrhetic shellfish toxins
ICHA2021, Mexico · 2021
Non-specific cyanobacteria bloom and microcystin detection in Abreus reservoir, Cuba
MOL2NET 2023, Paris/Ohio
Co-Author: Proteomics to disclose detoxification and immune system of Mytilus galloprovincialis
VI ICAP, Porto, Portugal · 2019
+ 15 additional contributions at international congresses (2009–2021)
Open Data
Datasets & Data Deposits
Pollicipes pollicipes proteomics datasets (S1–S3)
Mendeley Data · 2020
Lepas anatifera proteomics datasets (S1–S3)
Mendeley Data · 2021
Cerastoderma edule transcriptomics datasets (S1–S4)
Mendeley Data · 2021
Cephalopod salivary gland proteomics (S1–S9)
Mendeley Data · 2020
npj Biofilms proteomics data
ProteomeXchange / PRIDE · PXD029048 · 2022
MS/MS MALDI-TOF/TOF Microcystin toxins data
ResearchGate Supplementary · 2017
Academic
Teaching & Lecturing
Seminar: Proteogenómica como ferramenta no estudo de toxinas de animais — MSc Biotechnology & Synthetic Biology
Universidade do Porto, Faculdade de Ciências
Lecture: Proteogenómica e Toxicoproteómica — MSc Environmental Sciences
Universidade do Porto, Faculdade de Ciências
Lecturer — Animal Physiology (undergraduate)
Universidad Central Marta Abreu de Las Villas, Cuba
Teaching Assistant — Biophysics
Universidad de La Habana, Cuba
Mentoring
Supervision & Academic Juries
Student Supervision
| Period | Student / Topic | Role | Programme |
|---|---|---|---|
| 2020–2021 | Harold Casalís Cantalló — Ecophysiological and transcriptomic response of two intertidal molluscs to thermal stress | Supervisor | MSc Applied Marine Biology — Universidade de Aveiro / CIIMAR |
| 2017–2019 | Bachelor Thesis: Exposure of Mytilus galloprovincialis to diarrhetic shellfish toxins | Co-Supervisor | BSc Environmental Health — Instituto Politécnico do Porto |
| 2010–2012 | Yoel E. Tejeda Rodríguez — ECG signal analysis methodology in mice | Co-Supervisor | BSc Biomedical Engineering — UCLV, Cuba |
| 2010–2012 | Roberto Soler Parker — Etymological glossary of Cuban sea anemone species | Supervisor | BSc Biology — UCLV, Cuba |
Tutoring
Tomás Ferreira Costa Rodrigues
Jellyfish impact on aquatic ecosystems — early detection tools
Academic Juries
Member of 5 academic thesis juries at UCLV, Cuba (2011–2012), evaluating BSc theses in biology, ecology, and biomedical sciences.
Service
Peer Review & Scientific Service
Active reviewer for 16 indexed journals. Recognized as Exceptional Reviewer — Toxins 2025 Reviewers List (MDPI).
Toxins
MDPI · 2019–2025
Marine Drugs
MDPI · 2019
Antibiotics
MDPI
Genes
MDPI · 2019
IJMS
MDPI · 2021–2023
Scientific Reports
Nature · 2021
JMSE
MDPI · 2021
Comparative Biochemistry & Physiology C
Elsevier · 2020
Journal of Immunology Research
Hindawi · 2020
Toxics
MDPI · 2020
Proteomes
MDPI · 2020
Veterinary Sciences
MDPI · 2020
IJERPH
MDPI · 2020
Animals
MDPI · 2020
Cancers
MDPI · 2019
MOL2NET Conference
Sciforum/MDPI · 2020
Recognition
Awards & Distinctions
2025
Toxins Exceptional Reviewers List 2025
MDPI AG · Switzerland
2024
STSM Grant · Ref E-COST-GRANT-CA19144-EUVEN
CA19144 — European Venom Network (EUVEN) · Italy
2018
Cover Story Article — Marine Drugs 16(2):42
MDPI AG · Switzerland
2011
Grant — 1st Caribbean School of Neuroethology
International Brain Research Organization (IBRO) · France
2007
Best Oral Presentation — FBio-UH Annual Research Conference
Universidad de La Habana, Facultad de Biología
2007
Outstanding Student Award in Biophysics
Universidad de La Habana, Facultad de Biología
Memberships
International Society on Toxinology (IST) · Full Member since 2015
Latin American Association of Pharmacology (ALF) · Full Member since 2012
Cuban Society of Pharmacology (SCF) · Full Member since 2012
IUPHAR · Full Member since 2012
International Brain Research Organization (IBRO) · Alumni since 2011
Expertise
Core Expertise & Skills
OMICs & Marine Research
ProteotranscriptomicsVenomics & ToxinologyMarine EcotoxicologyBioactive Peptide DiscoveryDe novo Transcriptome AssemblyProteogenomicsAMP DiscoveryNon-model Organisms
Bioinformatics & Genomics
PythonR / BioconductorBash / Linux / HPCTrinityTrinotateTransDecoderBLAST / HMMERMAFFT / ClustalWIQ-TREE / MEGASTAR / HISAT2Salmon / Kallisto
Proteomics & Data Analysis
MaxQuantPEAKS / FragPipeProteome DiscovererMascotPerseusDESeq2 / edgeROmicsBox / Blast2GOSignalP 6.0InterPro / Pfam
Scientific Output
Manuscript WritingPeer ReviewGrant WritingSpecial Issue EditingStatistical AnalysisScience Communication
Teaching & Mentoring
University LecturingMSc SupervisionBioinformatics TrainingAcademic AdvisingThesis Juries
Business & Entrepreneurship
B2B Life SciencesBusiness DevelopmentBioinformatics ConsultingIberian MarketPagBiOmicS FounderBYOK AI Tools
Tools
Software Tools Authored
SeqLengthPlot v2.0
Python tool for FASTA sequence length visualization and retrieval with tunable splitting point. Published peer-reviewed.
Bioinformatics Advances, 2024FiltDeTox
Python tool for filtering and validating toxin candidates using mass spectrometry integration; reduces false positives in venomics pipelines.
GitHubConoServerParser
Parser for ConoServer database integration into venomics and conotoxin discovery pipelines.
OMICs Pipeline ToolkitDeepPeptideXtractor
Deep-learning-assisted extraction and classification of bioactive peptides from proteomes.
OMICs Pipeline ToolkitProtSpaceExtractor
Protein sequence space extraction tool for comparative proteomics and sequence diversity analysis.
OMICs Pipeline ToolkitTrinotateR-PfamFigs
R-based visualization of Trinotate/Pfam annotation outputs for non-model transcriptomes.
OMICs Pipeline ToolkitJobApp AI Assistant v0.2
Local-first BYOK job application assistant. CV parsing, job matching, application export. First d'BiYOK Lab app.
d'BiYOK Lab · GitHub ReleaseBioinformatics Stack
TrinityTransDecoderTrinotateAUGUSTUSBLAST+ / DIAMONDHMMERInterProScanSignalP 6.0OmicsBox / Blast2GOMAFFT / ClustalW / MUSCLEIQ-TREE / PhyMLSTAR / HISAT2Salmon / KallistoFastQC / TrimmomaticDESeq2 / edgeR / limmaMaxQuantPEAKS / FragPipeProteome DiscovererMascotPerseusGalaxyConda / Docker / SingularityGit / GitHub ActionsR + BioconductorPython / Biopython / PandasBash / HPC / SlurmConoServerAPD3CytoscapePrism / ggplot2
Languages
Languages
SpanishNative (C2)
PortugueseAdvanced (C1)
EnglishAdvanced (C1)
ItalianConversational (B1)
Academic Identifiers