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 2024M.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 2021B.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 – ongoingBiGeA Day 2023
University of Bologna, Bologna (IT). May 27, 2023University of Bologna opening days
University of Bologna, Bologna (IT). Nov 18, 2022
5. Professional skills
5.1. Bioinformatics
- Programming and markup languages
More
(beginner ▯▯▯▯▯ advantaced)bash
▮▮▮▮▯R
▮▮▮▯▯python
▮▮▯▯▯- LaTeX
▮▮▯▯▯ html
▮▯▯▯▯
- Phylogenetics
- 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
)
- Orthology inference (
- Mitogenomics
More
- Mitogenome assembly and annotation (
MitoHiFi
,MitoFinder
,mitoRNA
)
- Mitogenome assembly and annotation (
- Read manipulation
More
- Raw reads quality check (
FastQC
,MultiQC
) - Read trimming (
trimmomatic
) - Read mapping and filtering (
Bowtie2
,STAR
,TEtranscripts
,stringtie
,samtools
)
- Raw reads quality check (
- Transcriptomics
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 <a href=https://www.thermofisher.com/order/catalog/product/M7512)>MitoTracker</a>
- 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 <a href=/resources/>Resources</a> section of this website
6. Teaching experience
- Practical class “CAFE: estimating gene family turover 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 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 (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, 2023ITA*PHY phylogenetics workshop.
Trento (IT). Jun 6 – 9, 2023Sex chromosome evolution.
Physalia Courses.
Online. Jan 23 – 27, 2023Identification of butterflies from the Eastern Alps.
Dolimiti National Park.
Online. Mar 12 – Apr 2, 2022Science communication.
Feltrinelli Education.
Online. May 12 – Jun 3, 2021Nature illustration.
Associazione ARDEA.
Online. Feb 6 – Mar 20, 2021Advanced 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 2024Pasantes’ Lab.
University of Vigo, Vigo (ES). Jan 12 – 22, 2023
11. Society memberships
Italian Society for Evolutionary Biology (SIBE/ISEB)
Sep 2022 – ongoingSociety for Molecular Biology and Evolution (SMBE)
Jul 2023 – ongoingSociety for the Study of Evolution (SSE)
Jan 2023 – ongoingEuropean Society for Evolutionary Developmental Biology (EED)
Apr 2022 – ongoing