Dany Domínguez Pérez

Life Sciences & Clinical Business Development Representative - BIOMOL SL | Founder @ PagBiOmicS | PhD Biologist · NGS · RNAseq · Venomics · Proteogenomics · Biodiscovery

PhD Biologist · Marine Bioinformatics & OMICs · Scientific Sourcing & B2B

Porto, Portugal [email protected] pagbiomics.com ORCID: 0000-0002-5211-972X

Life Sciences Business Development Clinical Solutions NGS & RNA-seq Venomics Proteogenomics Biodiscovery PagBiOmicS Founder

455

Google Scholar Citations

h-index

i10-index

Journal Publications

Book Chapters

Conference Contributions

Languages

SpanishNative (C2)

PortugueseAdvanced (C1)

EnglishAdvanced (C1)

ItalianConversational (B1)

About

Research & Professional Profile

Dany is currently a Life Sciences & Clinical Business Development Representative at BIOMOL SL and Founder of PagBiOmicS. He is a PhD biologist and OMICs specialist working across NGS, RNA-seq, genomics, transcriptomics, proteomics, proteotranscriptomics, proteogenomics, venomics, and biodiscovery, primarily in non-model marine organisms. His career is positioned at the academic–industry interface, connecting advanced research, personalised scientific guidance, open-source software development, knowledge transfer, laboratory procurement, and life-sciences business development.

Trained in Biological Sciences at the University of Havana and awarded a PhD in Biology by the University of Porto, with a doctoral focus on bioinformatics, proteomics, transcriptomics, venomous animals, and evolutionary genomics. At CIIMAR — Interdisciplinary Centre of Marine and Environmental Research in Porto, doctoral research was developed within the Evolutionary Genomics and Bioinformatics (EGB) group, followed by research and infrastructure responsibilities within Blue Biotechnology and Ecotoxicology (BBE) and the Laboratory of Ecotoxicology, Genomics and Evolution (LEGE). At the Stazione Zoologica Anton Dohrn — National Institute of Marine Biology, Ecology and Biotechnology (SZN) in Naples, research was conducted within the Department of Biology and Evolution of Marine Organisms (BEOM).

CIIMAR · EGB / BBE–LEGE · Porto

Evolutionary genomics, infrastructure & experimental OMICs

Combined evolutionary genomics and venom research with coordination of the EMBRC-PT Molecular Biology and Proteomics platform, including equipment procurement and implementation, international user support, laboratory access, technical troubleshooting, and hands-on training. Within MOREBIVALVES, led workflows from aquarium preparation, bivalve maintenance, feeding, exposure and sampling through molecular sample preparation and integrative proteotranscriptomic biomarker analysis.

SZN · BEOM · Naples

Marine venomics, deep-sea biology & peptide biodiscovery

Within CRIMAC_DEEPVEN, developed and optimised advanced de novo transcriptomic, proteotranscriptomic, and toxin-discovery pipelines to characterise canonical and candidate venom repertoires in Mediterranean Anthozoa from mesophotic and deep-sea habitats, contributing to the discovery, prioritisation, and biological interpretation of peptides with ecological and biomedical potential.

PROQUINORTE / PagBiOmicS · Portugal & International

Scientific business development, market expansion & knowledge transfer

As the first employee recruited for PROQUINORTE’s expansion into Portugal, helped establish its initial commercial presence and customer base across research, biotechnology, diagnostic, and clinical-laboratory environments. Through PagBiOmicS, integrates OMICs consulting, research translation, technically informed procurement, partnership development, and knowledge exchange between scientific users, suppliers, and applied life-sciences organisations.

Cross-functional experience

End-to-end research delivery & international collaboration

Experience spans experimental design, marine-organism husbandry, molecular and proteomic sample processing, bioinformatics workflow development, statistical interpretation, data curation and repository deposition, manuscript and grant preparation, platform coordination, student supervision, scientific training, stakeholder engagement, and collaboration across multidisciplinary international teams.

Author or co-author of 20+ peer-reviewed publications in journals including Frontiers in Marine Science, npj Biofilms and Microbiomes, Marine Drugs, Toxins, Genomics, Bioinformatics Advances, and ACS Omega. Research contributions include early integrative proteotranscriptomic and proteogenomic workflows for biomarker and peptide discovery at a time when complete multi-stage OMICs pipelines were not yet routine in non-model marine organisms.

Author of open-source tools including SeqLengthPlot, ConoServerParser, FiltDeTox/ToxRecov, DeepPeptideExtractor, ProtSpaceExtractor, IdTabularFasta Extractor, and TrinotateR-PfamFigs. Professional experience also includes scientific sales, market expansion, account development, technical client support, needs assessment, supplier coordination, and laboratory procurement across Portugal and Spain. This dual academic and commercial perspective supports effective knowledge transfer: understanding the scientific requirements of researchers and laboratories while translating them into practical analytical, operational, procurement, and partnership solutions. PagBiOmicS brings these capabilities together through advanced OMICs analysis, tailored scientific support, research-to-application guidance, and B2B collaboration. Open to consulting, collaboration, and partnerships in bioinformatics, biodiscovery, marine biotechnology, diagnostics, and life sciences.

Career

Professional Experience

Life Sciences & Clinical Business Development Representative

BIOMOL SL · Portugal

3 Aug 2026 – Present

Represents BIOMOL SL’s Life Sciences and Clinical portfolio in Portugal, supporting commercial development across research, healthcare, and biotechnology environments.
Responsible for strategic account management and new client acquisition, developing relationships with research institutions, healthcare centres, biotechnology companies, and scientific laboratories.
Supports the distribution and market development of high-performance molecular diagnostics, biological reagents, and advanced OMICs solutions, translating scientific and clinical requirements into appropriate product and technical solutions.

Founder & Principal Bioinformatics Consultant

PagBiOmicS · Academic–Industry Interface · Porto / International

Feb 2026 – Present

Provides advanced OMICs analysis, bioinformatics consulting, personalised scientific guidance, and project design for researchers, biotechnology companies, and startups.
Connects scientific requirements with practical analytical, operational, procurement, and partnership solutions, supporting knowledge transfer between academia, biotechnology, diagnostics, and life-sciences suppliers.
Develops B2B opportunities involving laboratory reagents, molecular diagnostics, research procurement, technical support, and collaborative project development.
Developing d'BiYOK Lab: local-first, BYOK AI tools for researchers and professionals, including JobApp AI Assistant.

Research Fellow (Investigador)

Stazione Zoologica Anton Dohrn (SZN) — National Institute of Marine Biology, Ecology and Biotechnology · BEOM Department · Naples, Italy

Feb 2024 – Jan 2026

Developed and optimised RNA-seq, de novo transcriptomic, proteotranscriptomic, and toxin-discovery pipelines for Mediterranean Anthozoa collected from mesophotic and deep-sea habitats.
Characterised canonical and candidate toxin repertoires and prioritised novel bioactive peptides with ecological, pharmacological, and biomedical potential.
Curated sequence datasets and public deposits, and presented the Savalia savaglia toxin repertoire at EUVEN 2024.

Assistant Researcher & Co-Manager

CIIMAR — Interdisciplinary Centre of Marine and Environmental Research · BBE / LEGE · Porto, Portugal

Dec 2018 – May 2021

Led end-to-end experimental work in MOREBIVALVES: aquarium preparation, bivalve maintenance and feeding, exposure design, sampling, molecular and proteomics sample preparation, and integrative transcriptomic/proteomic analysis.
Investigated biomarkers and molecular responses associated with diarrhetic shellfish-toxin accumulation and depuration in commercial bivalves.
Managed laboratory activities, co-supervised students, supported reporting, and coordinated collaboration across experimental and analytical teams.

Research Assistant (Molecular Biology & Proteomics Platform)

CIIMAR — Interdisciplinary Centre of Marine and Environmental Research · EMBRC-PT · Porto, Portugal

Oct 2017 – Sep 2018

Coordinated the EMBRC-PT Molecular Biology and Proteomics platform, including equipment procurement and implementation, user support, laboratory access, and workflow organisation.
Supported international researchers and EMBRC fellows and delivered hands-on training in molecular-biology, sample-preparation, and proteomics workflows.

Account Manager & Business Development — Life Sciences

PROQUINORTE · Portugal Market Launch & Iberian Market

Apr 2022 – Mar 2023

First employee recruited for PROQUINORTE’s expansion into Portugal, independently supporting the establishment of its initial commercial presence and customer base.
Developed B2B relationships with universities, research centres, biotechnology organisations, diagnostic laboratories, clinical laboratories, and other life-sciences users.
Combined market prospecting, scientific sales, account development, technical presentations, needs assessment, quotations, commercial follow-up, and coordination with suppliers and the Spanish headquarters.
Translated scientific and laboratory requirements into suitable procurement solutions involving reagents, consumables, equipment, and diagnostic products, acting as an interface between scientific users, manufacturers, and commercial teams.

University Lecturer — Animal Physiology & Biological Fieldwork

Universidad Central Marta Abreu de Las Villas · Cuba

Sep 2009 – Jun 2012

Taught Animal Physiology and Biophysics at undergraduate level; coordinated Biological Fieldwork practical courses.

Training

Education & Training

PhD in Biology

University of Porto / CIIMAR · Evolutionary Genomics and Bioinformatics (EGB) · Portugal

2013 – 2017

FCT doctoral fellowship (SFRH/BD/80592/2011), developed within CIIMAR’s Evolutionary Genomics and Bioinformatics (EGB) group. Thesis: "Proteomics and Transcriptomics of Venomous Animals". Approved.

Degree in Biological Sciences (BSc)

Universidad de La Habana · Cuba

2004 – 2009

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

2009 – 2011

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 — Characterizing the Diversity and Activity of Venoms of Deep-Sea Anthozoa

Stazione Zoologica Anton Dohrn (SZN) · BEOM Department · Italian MUR

Feb 2024 – Jan 2026

Research Fellow within BEOM. Developed and applied transcriptomic, proteotranscriptomic, and bioinformatics pipelines to characterize venom repertoires and bioactive peptide candidates in Anthozoa from mesophotic and deep-sea Mediterranean habitats.

MOREBIVALVES — Molecular Strategies for Depuration of Commercial Bivalves

CIIMAR · BBE / LEGE · FCT · PTDC/ASP-PES/31762/2017

Dec 2018 – May 2021

Investigator within BBE/LEGE. Led bivalve exposure experiments, organism care and sampling, sample preparation, and integrated transcriptomic/proteomic analysis of diarrhetic shellfish-toxin responses.

EMBRC-PT — European Marine Biological Resource Centre

CIIMAR — Interdisciplinary Centre of Marine and Environmental Research · European Commission · EMBRC-1-2017-023

Oct 2017 – Sep 2018

Research Technical Fellow. Coordinated the EMBRC-PT Molecular Biology and Proteomics platform, including procurement support, implementation, researcher assistance, training, and technical workflows.

PhD Fellowship — Genomics of Venomous Animals from Cuba

FCT · University of Porto / CIIMAR · EGB · SFRH/BD/80592/2011

Dec 2012 – Nov 2016

Evolutionary Genomic Analyses of Toxic Cyanobacteria

CIIMAR · EGB · FCT · PTCRIS 104983

May 2010 – Oct 2013

Investigator within EGB. Contributed evolutionary-genomic analyses of molecular mechanisms associated with cyanotoxin response and detoxification across metazoan species.

Output

Peer-Reviewed Journal Publications

23 journal publications · 22 articles/reviews plus 1 editorial · Most recent first · Equal-contribution papers are identified below

Editorial: Harnessing Marine Biodiversity for Novel Antimicrobial Agents against Multidrug-Resistant Pathogens

Agüero-Chapin G, Domínguez-Pérez D, Marrero-Ponce Y · Frontiers in Microbiology 16 (2025) 1607539

Open AccessEditorial

SeqLengthPlot v2.0: an all-in-one, easy-to-use tool for visualizing and retrieving sequence lengths from FASTA files

Domínguez-Pérez D, Agüero-Chapin G, Leone S, Modica MV, DeGiorgio M · Bioinformatics Advances 5(1):vbae183 (2025; advance access 2024)

Open Access1 citation

Unveiling Encrypted Antimicrobial Peptides from Cephalopods Salivary Glands: A Proteolysis-Driven Virtual Approach

Agüero-Chapin G, Domínguez-Pérez D, Marrero-Ponce Y, Castillo-Mendieta K, Antunes A · ACS Omega (2024)

14 citationsCo-first author

Hydrodynamic Conditions Affect the Proteomic Profile of Marine Biofilms Formed by Filamentous Cyanobacterium

Romeu MJ, Domínguez-Pérez D, Almeida D, Morais J, Araújo MJ, Osório H, Campos A, Vasconcelos V, Mergulhão FJM · npj Biofilms and Microbiomes 8:80 (2022)

Open Access13 citationsCo-first author

Emerging Computational Approaches for Antimicrobial Peptide Discovery

Agüero-Chapin G et al., Domínguez-Pérez D · Antibiotics 11(7):936 (2022)

Open Access64 citations

Transcriptomic Profile of the Cockle Cerastoderma edule Exposed to Seasonal Diarrhetic Shellfish Toxin Contamination

Domínguez-Pérez D, Martins JC, Almeida D, Costa PR, Vasconcelos V, Campos A · Toxins 13(11):784 (2021)

Open Access10 citations

Quantitative Proteomic Analysis of Marine Biofilms Formed by Filamentous Cyanobacterium

Romeu MJ, Domínguez-Pérez D, Almeida D, Morais J, Araújo MJ, Osório H, Campos A, Vasconcelos V, Mergulhão FJM · Environmental Research 201:111566 (2021)

22 citationsCo-first author

Proteogenomic Characterization of the Cement and Adhesive Gland of the Pelagic Gooseneck Barnacle Lepas anatifera

Domínguez-Perez D, Almeida D, Wissing J, Machado AM, Jänsch L, Antunes A, Castro LF, et al. · IJMS 22(7):3370 (2021)

Open Access17 citations

Molecular Responses of Mussel Mytilus galloprovincialis Associated to Accumulation and Depuration of Marine Biotoxins Okadaic Acid and Dinophysistoxin-1 Revealed by Shotgun Proteomics

Martins JC, Domínguez-Pérez D, Azevedo C, Braga AC, Costa PR, Osório H, Vasconcelos VM, Campos A · Frontiers in Marine Science 7:589822 (2020)

Open Access22 citationsCo-first author

Data Employed in the Construction of a Composite Protein Database for Proteogenomic Analyses of Cephalopods Salivary Apparatus

Almeida D, Domínguez Pérez D, Matos A, Agüero-Chapin G, Castaño Guerrero Y, Vasconcelos V, Campos A, Antunes A · Data 5(4):110 (2020)

Open Access9 citationsCo-first author

Putative Antimicrobial Peptides of the Posterior Salivary Glands from the Cephalopod Octopus vulgaris Revealed by Exploring a Composite Protein Database

Almeida D, Domínguez-Pérez D, Matos A, Agüero-Chapin G, Osório H, Vasconcelos V, Campos A, Antunes A · Antibiotics 9(11):757 (2020)

Open Access21 citationsCo-first author

OMICs Approaches in Diarrhetic Shellfish Toxins Research

Campos A, Freitas M, de Almeida AM, Martins JC, Domínguez-Pérez D, Osório H, Vasconcelos V, Reis Costa P · Toxins 12(8):493 (2020)

Open Access30 citations

Characterization of Planktonic and Biofilm Cells from Two Filamentous Cyanobacteria Using a Shotgun Proteomic Approach

Romeu MJL, Domínguez-Pérez D, Almeida D, Morais J, Campos A, Vasconcelos V, Mergulhão FJM · Biofouling 36(6):631–645 (2020)

27 citationsCo-first author

Shotgun Proteomics of Ascidians Tunic Gives New Insights on Host–Microbe Interactions by Revealing Diverse Antimicrobial Peptides

Matos A, Domínguez-Pérez D, Almeida D, Agüero-Chapin G, Campos A, Osório H, Vasconcelos V, Antunes A · Marine Drugs 18(7):362 (2020)

Open Access17 citations

The Quantitative Proteome of the Cement and Adhesive Gland of the Pedunculate Barnacle Pollicipes pollicipes

Domínguez-Pérez D, Almeida D, Wissing J, Machado AM, Jänsch L, Castro LF, Antunes A, et al. · IJMS 21(7):2524 (2020)

Open Access26 citations

Medusozoans Reported in Portugal and its Ecological and Economical Relevance

Rodrigues T, Domínguez-Pérez D, Almeida D, Matos A, Antunes A · Regional Studies in Marine Science 35:101230 (2020)

25 citations

The Queen Conch (Lobatus gigas) Proteome: A Valuable Tool for Biological Studies in Marine Gastropods

Domínguez-Pérez D, Lippolis J, Dennis M, Miller B, Tiley K, Vasconcelos V, de Almeida AM, Campos A · The Protein Journal 38(6):628–639 (2019)

7 citations

Proteomic Analyses of the Unexplored Sea Anemone Bunodactis verrucosa

Domínguez-Pérez D, Campos A, Rodríguez AA, Turkina MV, Ribeiro T, Osorio H, Vasconcelos V, Antunes A · Marine Drugs 16(2):42 (2018)

Open Access37 citationsCover Story · Special IssueFlagship Paper

The Harderian Gland Transcriptomes of Caraiba andreae, Cubophis cantherigerus and Tretanorhinus variabilis, Three Colubroid Snakes from Cuba

Domínguez-Pérez D, Durban J, Agüero-Chapin G, Torres Lopez J, Molina Ruiz R, Almeida D, Calvete JJ, Vasconcelos V, Antunes A · Genomics (2018)

17 citations

Microcystin-LR Detected in a Low Molecular Weight Fraction from a Crude Extract of Zoanthus sociatus

Domínguez-Pérez D, Rodríguez A, Osorio H, Azevedo J, Castañeda O, Vasconcelos V, Antunes A · Toxins 9(3):89 (2017)

Open Access8 citations

Insights into the Toxicological Properties of a Low Molecular Weight Fraction from Zoanthus sociatus (Cnidaria)

Domínguez-Pérez D, Diaz-Garcia CM, García-Delgado N, Sierra-Gómez Y, Castañeda O, Antunes A · Marine Drugs 11(8):2873–2881 (2013)

Open Access15 citations

Toxins from Physalia physalis (Cnidaria) Raise the Intracellular Ca2+ of Beta-Cells and Promote Insulin Secretion

Diaz-Garcia CM, Fuentes-Silva D, Sanchez-Soto C, Dominguez-Perez D, García-Delgado N, Varela C, et al. · Current Medicinal Chemistry 19(31):5414–5423 (2012)

27 citations

Low Molecular Weight Compounds from Zoanthus sociatus Impair Insulin Secretion via Ca2+ Influx Blockade and Cause Glucose Intolerance in vivo

Diaz-Garcia CM, Sanchez-Soto C, Fuentes-Silva D, Leon-Pinzon C, Dominguez-Perez D, Varela C, Rodriguez-Romero A, Castañeda O, Hiriart M · Toxicon 59(2):306–314 (2012)

18 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 · DOI: 10.1201/9781351021821-15

2020

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

2013

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

Sep 2024

Avances en el estudio de la genómica de animales venenosos de Cuba

CYTED BIOTOX — IBV, Valencia, Spain

Jun 2014

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

+ 13 additional contributions at international congresses (2009–2021)

Open Data

Datasets & Data Deposits

Savalia savaglia paired-end RNA-seq and assembly outputs

Mendeley Data · Version 2 · 2024

Savalia savaglia ORFs and functional annotations

Mendeley Data · Version 4 · 2024

FiltDeTox classification of Savalia savaglia toxin candidates

Mendeley Data · Version 1 · 2025

Zibrowius primnoidus transcriptome resources

NCBI · BioProject PRJNA1223694 · SRA SRR32354500 · TSA GLCH00000000

Pollicipes pollicipes proteomics datasets (S1–S3)

Mendeley Data · 2020 · Representative record S1: 10.17632/bc65592ymt.1

Lepas anatifera proteomics datasets (S1–S3)

Mendeley Data · 2021 · Representative record S1: 10.17632/v2d3hvnycw.1

Cerastoderma edule transcriptomics datasets (S1–S4)

Mendeley Data · 2021 · Representative record S1: 10.17632/vkw2jcmmzt.1

Cephalopod salivary gland proteomics (S1–S9)

Mendeley Data · 2020 · Representative record S1: 10.17632/csc8shzkwc.1

npj Biofilms proteomics data

ProteomeXchange / PRIDE · PXD029048 · 2022

MS/MS MALDI-TOF/TOF Microcystin toxins data

Publisher supplementary data · 2017 · DOI: 10.3390/toxins9030089

Academic

Teaching & Lecturing

Invited postgraduate teaching · Universidade do Porto

Guest seminarFebruary 2020

Proteogenómica como ferramenta no estudo de toxinas de animais

MSc in Biotechnology and Synthetic Biology · Faculdade de Ciências, Universidade do Porto.

Guest lectureJune 2019

Proteogenómica e Toxicoproteómica

MSc in Environmental Sciences · Faculdade de Ciências, Universidade do Porto.

Undergraduate teaching · UCLV, Cuba

LecturerSep 2009 – Jun 2012

Animal Physiology

Undergraduate teaching, practical instruction, student assessment, and academic support in the Biology programme.

LecturerSep 2009 – Jun 2012

Biophysics

Teaching support linking physical principles with physiological processes, experimental measurements, and biological interpretation.

Course coordinator & instructorSep 2009 – Jun 2012

Biological Fieldwork

Coordinated field-based practical activities, sampling, biological observation, student supervision, and reporting for undergraduate Biology students.

Earlier university teaching · University of Havana

Teaching assistant2007 – 2009

Biophysics

Supported undergraduate practical classes and learning activities at the Faculty of Biology, University of Havana.

Mentoring

Supervision & Academic Juries

Student Supervision

Supervisor2020–2021

Harold Casalís Cantalló

Ecophysiological and transcriptomic response of two intertidal molluscs to thermal stress.

MSc Applied Marine Biology · Universidade de Aveiro / CIIMAR

Co-Supervisor2017–2019

Bachelor Thesis

Exposure of Mytilus galloprovincialis to diarrhetic shellfish toxins.

BSc Environmental Health · Instituto Politécnico do Porto

Co-Supervisor2010–2012

Yoel E. Tejeda Rodríguez

Methodology for ECG signal analysis in mice.

BSc Biomedical Engineering · UCLV, Cuba

Supervisor2010–2012

Roberto Soler Parker

Etymological glossary of Cuban sea anemone species.

BSc Biology · UCLV, Cuba

Research Tutoring

Research guidance

Tomás Ferreira Costa Rodrigues

Jellyfish impacts on aquatic ecosystems and the development of early-detection tools.

2017–2019

Academic Juries

5 BSc thesis juries UCLV, Cuba · 2011–2012

Evaluation of undergraduate theses in biology, ecology, and biomedical sciences.

Service

Peer Review & Scientific Service

Reviewer for 15 indexed journals and the MOL2NET scientific conference. Recognized in the Toxins 2025 Exceptional 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

Six integrated domains combining experimental biology, marine research, OMICs, bioinformatics, scientific leadership, and academic–industry experience. Related methods, software, databases, and repositories are grouped within each domain to avoid repetition.

OMICs, Bioinformatics & Peptide Biodiscovery

Integrated multi-omics workflows for non-model organisms, venom systems, and bioactive peptides.

Core expertise

Methods & software

Marine Biodiversity, Ecotoxicology & Environmental Biomarker Discovery

Experimental marine biology linking organismal responses, biotoxin exposure, and molecular biomarkers.

Core expertise

Analysis & visualisation

Experimental Biology, Molecular Methods & Functional Assays

Wet-lab experimentation from molecular sample processing to organismal and pharmacological evaluation.

Core expertise

Computational Research, Data Curation & Repositories

Reproducible analysis, workflow automation, scientific data stewardship, and public deposition.

Programming & computing

Curation, repositories & knowledgebases

Scientific Leadership, Teaching & Communication

Coordination of research, infrastructure, training, mentoring, publishing, and collaborative scientific delivery.

Core expertise

Academic–Industry Interface, Knowledge Transfer & Entrepreneurship

Connecting scientific needs with consulting, procurement, commercial development, partnerships, and applied solutions.

Core expertise

Tools

Software Tools Authored

SeqLengthPlot v2.0.2

Python command-line tool for FASTA length analysis, configurable sequence splitting and retrieval, summary statistics, and publication-ready linear or logarithmic distributions.

Bioinformatics Advances, 2025

FiltDeTox / ToxRecov

Post-processing and sequence-recovery workflow that combines DeTox classifications, secretion predictions, HMMER toxin-family evidence, Pfam domains, and annotation support to reduce false positives and recover full-length candidates.

GitHub

ConoServerParser

R/Shiny workflow for filtering ConoServer records, exporting mature-peptide FASTA files and grouped datasets, and generating summary visualizations for conotoxin research.

OMICs Pipeline Toolkit

DeepPeptideExtractor

Parses DeepPeptide predictions, extracts mature peptide products, handles multiple products per precursor, and removes very short sequences.

OMICs Pipeline Toolkit

ProtSpaceExtractor

Ranks candidate peptides by proximity to reference neurotoxins across PCA, UMAP, and t-SNE protein-sequence spaces using multi-method consensus evidence and automated reports.

OMICs Pipeline Toolkit

IdTabularFasta Extractor

R/Shiny application for exact, substring, or regex-based extraction across multiple tables, FASTA files, and identifier lists, with inclusion/exclusion logic and visual quality-control reports.

Data Integration Toolkit

TrinotateR-PfamFigs

R workflow for summarizing and visualizing Trinotate and Pfam annotations in de novo transcriptomes from non-model organisms.

OMICs Pipeline Toolkit

JobApp AI Assistant v0.2

Local-first BYOK assistant for structured CV parsing, job matching, application development, and export.

d'BiYOK Lab

Profiles & Links

Academic Identifiers

Ciência ID

0A12-DF56-155A

ORCID iD

0000-0002-5211-972X

Scopus Author ID

54902002000

Languages

Research & Professional Profile

Evolutionary genomics, infrastructure & experimental OMICs

Marine venomics, deep-sea biology & peptide biodiscovery

Scientific business development, market expansion & knowledge transfer

End-to-end research delivery & international collaboration

Professional Experience

Education & Training

Projects & Grants

Peer-Reviewed Journal Publications

Book Chapters

Conference Contributions

Datasets & Data Deposits

Teaching & Lecturing

Proteogenómica como ferramenta no estudo de toxinas de animais

Proteogenómica e Toxicoproteómica

Animal Physiology

Biophysics

Biological Fieldwork

Biophysics

Supervision & Academic Juries

Harold Casalís Cantalló

Bachelor Thesis

Yoel E. Tejeda Rodríguez

Roberto Soler Parker

Tomás Ferreira Costa Rodrigues

Peer Review & Scientific Service

Awards & Distinctions

Core Expertise & Skills

Software Tools Authored

SeqLengthPlot v2.0.2

FiltDeTox / ToxRecov

ConoServerParser

DeepPeptideExtractor

ProtSpaceExtractor

IdTabularFasta Extractor

TrinotateR-PfamFigs

JobApp AI Assistant v0.2

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LinkedIn

PagBiOmicS

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