Curriculum Vitae Highlights
Last updated: Aug 11, 2026
Find the extended version of my CV at this link.
Outlook
Employment
Research Associate
Subject: Evolution of the phototransduction machinery in early metazoans.
Supervisor: prof. Roberto Feuda
University of Leicester, Leicester (UK). Nov 2024–ongoing
Education
Ph.D in "Innovative technologies and sustainable use of Mediterranean Sea fishery and biological resources" (FishMed-PhD)
Thesis: Integrative perspectives on bivalve sex determination: A comparative and evolutionary analysis across phylogeny
Supervisor: prof. Andrea Luchetti
University of Bologna, Bologna (IT). Nov 2021–Oct 2024
M.Sc in "Biodiversity and evolution"
Thesis: Identification of Hox and ParaHox genes in tadpole shrimp genomes (Pancrustacea, Branchiopoda, Notostraca)
Supervisor: prof. Andrea Luchetti
University of Bologna, Bologna (IT). Sep 2019–Jul 2021
B.Sc in "Biological Sciences"
Thesis: Species delimitation and phylogenetic analysis of the Australian genus Candovia (Insecta, Phasmida)
Supervisor: prof. Barbara Mantovani
University of Bologna, Bologna (IT). Sep 2016–Oct 2019
Professional skills
Bioinformatics
Programming and command languages. Fluent in bash, R, and python for data analysis and pipeline development; comfortable with LaTeX and html for scientific writing and web work. I also use Snakemake and git.
Single-cell transcriptomics. Extensive experience from mapping and pre-processing (CellRanger, pipseeker, Seurat) to functional and comparative analysis (hdWGCNA, scVelo, SAMap, metacell).
Comparative genomics. Focused on how gene families originate, expand, and diversify over evolutionary time, including orthology inference (OrthoFinder, possvm), gene annotation (BLAST, InterProScan), molecular evolution and selection analysis (PAML, HyPhy), and gene family dynamics (CAFE5, GeneRax).
Phylogenomics. Maximum-likelihood and Bayesian tree inference (IQTREE, PhyloBayes), advanced multiple sequence alignment (MAFFT, ClustalO, trimAl), and time-tree calibration (MCMCTree).
Bulk transcriptomics. Differential expression analysis (DESeq2, maSigPro).
High-throughput sequencing. Short- and long-read data (Trinity, STAR, hifiasm, MitoHiFi).
Wet-lab
mRNA in-situ HCR and Immunofluorescence. Extensive experience across whole-mount materials (bivalve embryos and larvae, zebrafish larvae, sea urchin embryos, placozoans) and excised tissues/organs (sponges, ctenophores). Routinely run multiplexed HCR experiments and design probes in-house. Independent user of advanced confocal systems (Zeiss LSM 980 with Airyscan 2, Stellaris 5). Confident with ImageJ/Fiji for image analysis, plus experience with phase-contrast microscopy.
Single-cell/-nucleus transcriptomics. Actively developing protocols to isolate single cells/nuclei from challenging tissue types, handling both fresh and flash-frozen material. Confident with Illumina PIPseq chemistry.
Culture of marine and terrestrial animals. Rear marine species including bivalves, placozoans, and the starlet sea anemone (Nematostella vectensis), as well as single-celled algae and Artemia nauplii as food sources. Perform controlled spawning and in-vitro fertilization of bivalves and the starlet sea anemone. Also rear terrestrial animals, including stick insects (Phasmatodea) and webspinners (Embioptera).
Tissue and organ dissections. Excise tissues and organs across animal samples, with particular experience in ant cephalic ganglia and pre-pupae, ctenophore aboral organs, epidermis and gut, and sponge cross-sections.
Metaphase-plate chromosome preparation. Obtain chromosome metaphase plates from several animals, including ants and bivalves.
Outreach activity
For a more detailed description of my outreach activity, have a look at the Outreach section of this website.
- Co-lead of the "Foster capacity building via accessible and inclusive training pro-grammes" Working Group of the "CONSENSA" COST Action
Sep 2026–ongoing - Co-coordinator of the dissemination program for the project Wood Wide Ants
University of Bologna. Bologna, Italy. Jul 2024–ongoing - Member of the "Community Engagement" Committee by ERGA
ERGA. Sep 2025–ongoing - Editor and web writer
BioPills. Jul 2017–ongoing
Teaching experience
- Practical class "CAFE: estimating gene family turnover across a phylogenetic tree"
Master degree in Bioinformatics
University of Bologna.
Bologna, Italy. Apr 23, 2024 - Practical invertebrate zoology class
Bachelor degree in Biological Sciences
University of Bologna.
Bologna, Italy. Sep 2022–Jan 2023
Publications
Nicolini F, Nuzhdin SV, Ghiselli F, Luchetti A, & Milani L. (2026). Early embryonic transcription of Vasa in the Mediterranean mussel reveals divergent routes to germline specification in bivalves. Under revision. 10.21203/rs.3.rs-9824110/v1
Goulty M, Lewis C, Nicolini F, Khalid R, Syed H, Oliveri P, Thomas MG, Rosato E, & Feuda R. (2025). Monoaminergic neurons share transcriptional identity across Bilaterian animals. Under revision. doi: 10.1101/2025.10.10.679534
Forni G, Fusco G, Nicolini F, Bruce H, & Luchetti A (2026). Loss, persistence and reversal of phenotypic traits. Biological Reviews. doi: 10.1002/brv.70168
Forni G*, Nicolini F*, Martelossi J, Savojardo C, Corneti S, Marrone F, & Luchetti, A. (2026). The elusive genomic signature of tadpole shrimps’ ancient morphology. Biology Letters, 22(3), 20250130. doi: 10.1098/rsbl.2025.0130
Iannello M, Piccinini G, Salatiello F, Forni G, Nicolini F, Valdrè U, Martini M, Martelossi J, Ghiselli F, D’Aniello E, & Milani L. (2025). New insights into mitochondrial segregation from the Doubly Uniparental Inheritance system in bivalves. BMC Biology, 23(1), 371. doi: 10.1186/s12915-025-02459-6
Nicolini F, Nuzhdin SV, Ghiselli F, Luchetti A, & Milani L (2025). Comparative genomics of sex‐determination‐related genes reveals shared evolutionary patterns between bivalves and mammals, but not fruit flies. Molecular Ecology, 34(20), e70103. doi: 10.1111/mec.70103
Righetti N*, Nicolini F*, Forni G, & Luchetti A. (2025). Towards a time-tree solution for Branchiopoda diversification: a jackknife assessment of fossil age priors. Palaeoentomology, 8(3), 316-328. doi: 10.11646/palaeoentomology.8.3.8
Nicolini F, Ghiselli F, Luchetti A, & Milani L. (2023). Bivalves as emerging model systems to study the mechanisms and evolution of sex determination: a genomic point of view. Genome Biology and Evolution, 15(10), evad181. doi: 10.1093/gbe/evad181
Martelossi J, Nicolini F, Subacchi S, Pasquale D, Ghiselli F, & Luchetti A. (2023). Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution. BMC Biology, 21(1), 1-23. doi: 10.1186/s12915-023-01632-z
Nicolini F, Martelossi J, Forni G, Savojardo C, Mantovani B, & Luchetti A. (2023). Comparative genomics of Hox and ParaHox genes among major lineages of Branchiopoda with emphasis on tadpole shrimps. Frontiers in Ecology and Evolution, 11, 23. doi: 10.3389/fevo.2023.1046960
Forni G, Cussigh A, Brock PD, Jones BR, Nicolini F, Martelossi J, ... & Mantovani B. (2023). Taxonomic revision of the Australian stick insect genus Candovia (Phasmida: Necrosciinae): insight from molecular systematics and species-delimitation approaches. Zoological Journal of the Linnean Society, 197(1), 189-210. doi: 10.1093/zoolinnean/zlac074
* equal contribution
Oral presentations at congresses
For a report of poster presentations, have a look at the Resources section of this website.
- Nicolini F, La Rodé D, Aleotti A, Devilliers JSA, Kay C, Pisani D, Feuda R. (2026). Tracing the evolutionary origin of the animal phototransduction toolkit through comparative genomics and single-cell transcriptomics. Joint meeting of the Italian Zoological Union (UZI) and the Italian Protistology Society (SIP).
Milan, Italy. Sep 8–11, 2026 - Nicolini F, Iannello M, Piccinini G, Ghiselli F, Luchetti A, Milani L. (2024). Advancing the study of bivalve sex determination in the light of comparative genomics. Establishing state-of-the-art mollusc genomics (EMBO workshop).
Namur, Belgium. May 27–30, 2024. - Nicolini F, Ghiselli F, Milani L, Luchetti A. (2023). Contrasting patterns of amino acid evolution and shared ancestry between putative sex-determining genes in bivalve molluscs. EVOLMAR 2023.
Online. Nov 14–17, 2023. - Nicolini F, Ghiselli F, Milani L, Luchetti A. (2023). Sex-determination related genes in bivalves: novel acquisitions and high rates of sequence evolution. Evolution 2023 (Ernst Mayr Award symposium).
Online. Jun 2–3, 2023.
Invited talks and seminars
- Nicolini F. (2025). Beyond sex chromosomes: how sexual processes shape genomes and molecules. Seminar for the course "Evoluzione del Genoma", Master degree in "Biodiversità ed Evoluzione". University of Bologna. Bologna, Italy. Nov 28, 2025.
- Nicolini F. (2025). Nomi, cose, città: come parlare di scienza? L’importanza del linguaggio nella comunicazione. Seminar for the online course "Divulgare la scienza: Istruzioni per l’uso", organised by BioPills. Online. Nov 9, 2025.
- Nicolini F. (2024). From comparative genomics to fluorescence imaging: a multi-disciplinary approach to study bivalve sex determination. Department of Biology seminar series. University of Fribourg. Fribourg, Switzerland. Jul 26, 2024.
- Nicolini F, Chignoli D. (2021). Communicators are not improvised — BioPills in a nutshell. In the event: How to simplify science without inaccuracies. Institute for Research in Biomedicine (IRB) Barcelona. Online. Jun 15, 2021.
- Licari G, Chignoli D, Bencardino D, Nicolini F (2021). In the event: Scienze e Social: tra informazione e pericolo.. Vivere Ateneo, Univeristy of Palermo. Online. Apr 20, 2021.
Courses and workshops
- Introduction to ImageJ/Fiji.
Advanced Imaging Facility, University of Leicester.
Leicester, UK. Jul 27, 2026. - New techonologies for developmental evolutionary biology studies.
Spanish Society of Evolutionary Biology (SESBE).
Madrid, Spain. Dec 16–19, 2024. - Establishing state-of-the-art mollusc genomics
EMBO Workshop. Awarded with a travel grant.
Namur, Belgium. May 28–31, 2024. - Art (Science) Attack
Physalia Courses.
Online. May 20–23, 2024. - Introduction to Python for biologists
Physalia Courses.
Online. Sep 25–28, 2023 - ITA*PHY phylogenetics workshop
Trento (IT). Jun 6–9, 2023 - Sex chromosome evolution
Physalia Courses.
Online. Jan 23–27, 2023 - Science communication
Feltrinelli Education.
Online. May 12–Jun 3, 2021 - Advanced Open Water Diver (PADI Education)
Scientific Diving School (SDS).
Bologna, Italy. Oct 18, 2020
Awards and scholarships
- Travel grant to attend the "Evoluzione 2024" congress in Naples, Italy.
Issued by Stazione Zoologica Anton Dohrn. Amount: € 250.00.
May 28–31, 2024 - Travel grant to attend the EMBO workshop "Establishing state-of-the-art mollusc genomics" in Namur (Belgium).
Issued by EMBO. Amount: € 500.00.
May 28–31, 2024 - Marco Polo scholarship to promote the scientific training of young researchers and offer the opportunity to carry out research in an international context.
Issued by the University of Bologna. Amount: € 4,050.00.
Apr 13, 2023 - Laura Bassi scholarship for editorial assistance to postgraduates and junior academics.
Issued by Editing Press. Amount: $ 500.00.
Apr 13, 2023 (Spring edition)
Visiting scholar
- Nuzhdin's Lab
University of Southern California.
Los Angeles, California, USA. Aug 2023–Feb 2024 - Pasantes' Lab
University of Vigo.
Vigo, Spain. Jan 12–22, 2023