Curriculum Vitae

Last updated: Jun 3, 2024

Please find an extended version of my CV in this link.

1. Education

• Ph.D in “Innovative technologies and sustainable use of Mediterranean Sea fishery and biological resources” (FishMed-PhD), University of Bologna, 2025 (expected)
  Subject: Comparative genomics of bivalve sex-determination related genes
  Supervisor: prof. Andrea Luchetti
• M.Sc in “Biodiversity and evolution”, University of Bologna, 2021
  Thesis: Identification of Hox and ParaHox genes in tadpole shrimp genomes (Pancrustacea, Branchiopoda, Notostraca)
  Supervisor: prof. Andrea Luchetti
• B.Sc in “Biological Sciences”, University of Bologna, 2019
  Thesis: Species delimitation and phylogenetic analysis of the Australian genus Candovia (Insecta, Phasmida)
  Supervisor: prof. Barbara Mantovani

2. Publications

• 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

3. Outreach activity

For a more detailed description of my outreach commitment, please have a look also at the Outreach section in this website.

• Editor and web writer, BioPills
  Jul 2017 – ongoing

• BiGeA Day 2023, University of Bologna
  May 27, 2023

• University of Bologna opening days
  Nov 18, 2022

4. Professional skills

4.1. Bioinformatics

• Programming and command languages (beginner ∘∘∘∘∘ advantaced)
  • bash
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  • R
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  • python
    ●●∘∘∘
  • $\LaTeX$
    ●∘∘∘∘
  • html
    ●∘∘∘∘
• Phylogenetics
  • ML phylogenetic analysis (IQTREE, RAxML-NG, FastTree)
  • Bayesian phylogenetic analysis (MrBayes, PhyloBayes)
  • Global alignment tools (MAFFT, MUSCLE, Clustal Omega, trimAl, GBlocks)
  • Tree calibration (lsd2, MCMCTree)
  • Tree decomposition (DISCO)
• Comparative genomics
  • Orthology inference (OrthoFinder, Possvm, TOGA)
  • Gene annotation (BLAST, DIAMOND, HMMER, InterProScan, tRNAscan-SE)
  • Genome quality assessment (BUSCO)
  • Molecular evolution (PAML, HyPhy, BASE, RRTree)
  • Gene family evolution (CAFE5, GeneRax)
  • Gene macro-synteny (MCScanX/JCVI)
  • Detection of sex-related loci (SEX-DETector, SDpop)
  • Other (AGAT, GffRead)
• Mitogenomics
  • Mitogenome assembly and annotation (MitoHiFi, MitoFinder, mitoRNA)
• Read manipulation
  • Raw reads quality check (FastQC, MultiQC)
  • Read trimming (trimmomatic)
  • Read mapping and filtering (Bowtie2, STAR, TEtranscripts, stringtie, samtools)
• Transcriptomics
  • De-novo transcriptome assembly (Trinity)
  • Gene differential expression (NOISeq, DESeq2, maSigPro, topGO)

4.2. Wet-lab

• Metaphase-plate chromosome preparation
  • Experience with bivalves and ants
• Total DNA extraction
  • Experience with insects
• Polymerase Chain Reaction (PCR)
  • Experience with insect mitochondrial and nuclear markers
• Mediterranean mussel (Mytilus galloprovincialis) embryology
  • Spawning induction by thermal shock
  • Gamete collection and concentration
  • Sperm mitochondria staining with MitoTracker
  • In-vitro fertilization of eggs
  • Embryo rearing in flasks or multi-well plates
  • Estimation of survival rates
• Hybridization Chain Reaction with RNA Fluorescence In-Situ Hybridization (HCR RNA-FISH)
  • Experience with whole-mount embryos of the Mediterranean mussel (Mytilus galloprovincialis)
  • Probe design
  • Multiplex experiments (up to four target genes), paired with DAPI and MitoTracker stainings
  • Confocal imaging
  • Experience with Leica DMi8 paired with Stellaris 5 systems

4.3. Others

• Field scientific sampling
  • Experience with termites, ants, and freshwater crustaceans
  • Experience with mussels and oysters
  • Field sample storing for subsequent DNA extraction (pure methanol) or mRNA extraction (RNAlater or Trizol)
• Scientific illustration (see the Resources section of this website)

5. Teaching experience

• Practical class “CAFE: estimating gene family turover across a phylogenetic tree”
  Master degree in Bioinformatics
  Apr 23, 2024
• Practical invertebrate zoology class
  Bachelor degree in Biological Sciences
  Sep 2022 – Jan 2023

6. Oral presentations at congresses

For a report of poster presentations, please have a look also at the Resources section in this website.

• 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. 4

• 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.

7. Courses and workshops

• 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, Italy. Jun 6 – 9, 2023

• Sex chromosome evolution.
  Physalia Courses.
  Online. Jan 23 – 27, 2023

• Identification of butterflies from the Eastern Alps.
  Dolimiti National Park.
  Online. Mar 12 – Apr 2, 2022

• Science communication.
  Feltrinelli Education.
  Online. May 12 – Jun 3, 2021

• Nature illustration.
  Associazione ARDEA.
  Online. Feb 6 - Mar 20, 2021

• Advanced Open Water Diver (PADI Education).
  Scientific Diving School (SDS).
  Bologna, Italy. Oct 18, 2020

8. Awards and scholarships

• Travel grant to attend the EMBO workshop “Establishing state-of-the-art mollusc genomics” in Namur (Belgium).
  EMBO.
  May 28 - 31, 2024
• Laura Bassi scholarship for editorial assistance to postgraduates and junior academics.
  Editing Press.
  Apr 13, 2023

9. Visiting scholar

• Nuzhdin’s Lab.
  University of Southern California. Los Angeles, California, USA.
  Aug 20, 2023 – Feb 20, 2024

• Pasantes’ Lab.
  University of Vigo. Vigo, Spain.
  Jan 12 – 22, 2023

10. Society memberships

• Italian Society for Evolutionary Biology (SIBE/ISEB)
  Sep 2022 – ongoing

• Society for Molecular Biology and Evolution (SMBE)
  Jul 2023 – ongoing

• Society for the Study of Evolution (SSE)
  Jan 2023 – ongoing

• European Society for Evolutionary Developmental Biology (EED)
  Apr 2022 – ongoing