Curriculum Vitae

Last updated: Dec 2, 2024

Find the extended version of my CV in this link.

1. Professional experience

Research Associate
Subject: Evolution of vision in early metazoans.
Supervisor: prof. Roberto Feuda
University of Leicester, Leicester (UK). Nov 2024 - ongoing

2. 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

3. 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

4. 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, Bologna (IT). May 27, 2023
• University of Bologna opening days
  University of Bologna, Bologna (IT). Nov 18, 2022

5. Professional skills

5.1. Bioinformatics

• Programming and markup languages
  More

  (beginner ▯▯▯▯▯ advanced)

  • bash
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  • R
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  • python
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  • LaTeX
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  • html
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• Phylogenetics
  More

  • 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
  More

  • 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
  More

  • Mitogenome assembly and annotation (MitoHiFi, MitoFinder, mitoRNA)
• Read manipulation
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  • Raw reads quality check (FastQC, MultiQC)
  • Read trimming (trimmomatic)
  • Read mapping and filtering (Bowtie2, STAR, TEtranscripts, stringtie, samtools)
• Transcriptomics
  More

  • De-novo transcriptome assembly (Trinity)
  • Gene differential expression (NOISeq, DESeq2, maSigPro, topGO)

5.2. Wet-lab

• Metaphase-plate chromosome preparation
  More

  • Experience with bivalves and ants
• Total DNA extraction
  More

  • Experience with insects
• Polymerase Chain Reaction (PCR)
  More

  • Experience with insect mitochondrial and nuclear markers
• Mediterranean mussel (Mytilus galloprovincialis) embryology
  More

  • 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
• mRNA in-situ Hybridization Chain Reaction (mRNA in-situ HCR)
  More

  • 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 (main experience with Leica DMi8 paired with Stellaris 5 systems)

5.3. Others

• Field scientific sampling
  More

  • 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

6. Teaching experience

• Practical class "CAFE: estimating gene family turnover across a phylogenetic tree"
  Master degree in Bioinformatics
  University of Bologna, Bologna (IT). Apr 23, 2024
• Practical invertebrate zoology class
  Bachelor degree in Biological Sciences
  University of Bologna, Bologna (IT). Sep 2022 – Jan 2023

7. Oral presentations at congresses

For a report of poster presentations, please have a look also at the Resources section of 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 (BE). 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.

8. 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 (IT). 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 (IT). Oct 18, 2020

9. 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

10. Visiting scholar

• Nuzhdin's Lab
  University of Southern California, Los Angeles (CA, USA). Aug 2023 – Feb 2024
• Pasantes' Lab
  University of Vigo, Vigo (ES). Jan 12 – 22, 2023

11. 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