SERENA ROSIGNOLI

PhD Student

PhD program:: XXXVII
email: serena.rosignoli@uniroma1.it
phone: 0649910913
building: CU027
room: T1A

supervisor: Alessandro Paiardini
advisor: Alessandro Paiardini

Research: Development of protein modeling and drug design platforms for assisting structural bioinformatics.

EDUCATION

October 2019 – June 2021

Master Degree in Genetics and Molecular Biology (English curriculum, LM-6) - Path of excellence - “Università degli studi di Roma La Sapienza” - 110/110 with honors

October 2016 – October 2019

Bachelor’s Degree in Biotechnology (L-2) - “Università degli studi di Roma La Sapienza” - 110/110 with honors

PHD (XXXVII)
Curriculum: Bioinformatics and Omics, Structure and function of macromolecules, Drug Discovery.

RESEARCH PROJECTS:

- Avvio alla Ricerca 2023: A Modular Computational Platform for PPI-Targeted Design and Ab-initio Modeling of D-Peptides binders; Serena Rosignoli; Sapienza; 1.308 €
- Avvio alla Ricerca 2022: A Computational Platform for Allele-specific, Custom-Designed CRISPR/Cas Proteins and its Application in the Treatment of Autosomal Dominant Disorders; Serena Rosignoli; Sapienza; 1.250 €

CONFERENCES:
Poster presentation @EMBO Workshop - Computational structural biology; EMBL Advanced Training Center; Heidelberg (DE); Dec. 2023.
Speaker @ELIXIR 3D-Bioinfo and 3D-SIG Conference in Structural Bioinformatics; Prague (CZ); November 2023.
Lecturer @MedILS Summer School in Bioinformatics; Split (HR); Aug. 2023.
Poster presentation @SBDD-Computational Advances in Drug Discovery; Sestri Levante (IT); May 2023.
Speaker @ELIXIR 3D-Bioinfo Annual Meeting; EMBL-EBI, Hinxton (UK); Nov. 2022.
Lecturer @CIVIS Summer School - Bioinformatics for non-bioinformaticians; Tübingen (DE); Jul. 2022.

TECHNICAL SKILLS AND COMPETENCES

- Object Oriented programming (OOP) in Python (Software and GUI development)
- Advanced usage of ‘in silico’ chemical tools for molecular visualization and manipulation (PyMOL, MarvinSketch, Openbabel, RDKit)
- Detailed theoretical and practical knowledge of Molecular Docking algorithms and related programs
- Bioinformatic analyses on Mass-Spectrometry-derived data.
- Linux, macOS and Windows Operative Systems use and management (software updates, programs installation)
- Good level of knowledge of Bash and R programming languages
- Protein structure prediction (Homology Modeling)

Research products

11573/1701072 - 2024 - Identification of the pyridoxal 5′‐phosphate allosteric site in human pyridox(am)ine 5′‐phosphate oxidase

Barile, Anna; Graziani, Claudio; Antonelli, Lorenzo; Parroni, Alessia; Fiorillo, Annarita; Di Salvo, Martino Luigi; Ilari, Andrea; Giorgi, Alessandra; Rosignoli, Serena; Paiardini, Alessandro; Contestabile, Roberto; Tramonti, Angela - 01a Articolo in rivista

paper: PROTEIN SCIENCE (Cambridge University Press / New York:40 West 20th Street:New York, NY 10011:(800)872-7423, (212)924-3900, EMAIL: journals_subscriptions@cup.org, INTERNET: http://www.journals.cambridge.org, Fax: (212)691-3239) pp. - - issn: 0961-8368 - wos: WOS:001146773300001 (2) - scopus: 2-s2.0-85182849034 (2)

11573/1711262 - 2024 - AlPaCas: allele-specific CRISPR gene editing through a protospacer-adjacent-motif (PAM) approach

Rosignoli, Serena; Lustrino, Elisa; Conci, Alessio; Fabrizi, Alessandra; Rinaldo, Serena; Latella, Mariacarmela; Enzo, Elena; Prosseda, Gianni; De Rosa, Laura; De Luca, Michele; Paiardini, Alessandro - 01a Articolo in rivista

paper: NUCLEIC ACIDS RESEARCH (Oxford University Press:Journals Department, Great Clarendon Street, Oxford OX2 6DP United Kingdom:011 44 1865 556767, EMAIL: jnlorders@oup.co.uk, INTERNET: http://www.oup.co.uk, Fax: 011 44 1865 267485 Editore precedente: Information Retrieval ltd., London) pp. W29-W38 - issn: 0305-1048 - wos: WOS:001230689400001 (0) - scopus: 2-s2.0-85197797884 (1)

11573/1707220 - 2024 - Making Use of Averaging Methods in MODELLER for Protein Structure Prediction

Rosignoli, Serena; Lustrino, Elisa; Di Silverio, Iris; Paiardini, Alessandro - 01a Articolo in rivista

paper: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (Basel: MDPI Center) pp. 1-20 - issn: 1422-0067 - wos: WOS:001160493200001 (1) - scopus: 2-s2.0-85184717314 (1)

11573/1720302 - 2024 - An outlook on structural biology after AlphaFold: tools, limits and perspectives

Rosignoli, Serena; Pacelli, Maddalena; Manganiello, Francesca; Paiardini, Alessandro - 01g Articolo di rassegna (Review)

paper: FEBS OPEN BIO (Hoboken NJ: Wiley & Sons Amsterdam : Elsevier) pp. 1-21 - issn: 2211-5463 - wos: WOS:001318796000001 (0) - scopus: 2-s2.0-85204642946 (0)

11573/1729153 - 2024 - Off-target inhibition of human dihydroorotate dehydrogenase (hDHODH) highlights challenges in the development of fat mass and obesity-associated protein (FTO) inhibitors

Tarullo, M.; Fernandez Rodriguez, G.; Iaiza, A.; Venezia, S.; Macone, A.; Incocciati, A.; Masciarelli, S.; Marchioni, M.; Giorgis, M.; Lolli, M. L.; Fornaseri, F.; Proietti, L.; Grebien, F.; Rosignoli, S.; Paiardini, A.; Rotili, D.; Mai, A.; Bochenkova, E.; Caflisch, A.; Fazi, F.; Fatica, A. - 01a Articolo in rivista

paper: ACS PHARMACOLOGY & TRANSLATIONAL SCIENCE (Washington DC: American Chemical Society) pp. - - issn: 2575-9108 - wos: WOS:001366197700001 (0) - scopus: 2-s2.0-85210408199 (0)

11573/1691811 - 2023 - PyPCN: protein contact networks in PyMOL

Rosignoli, Serena; Di Paola, Luisa; Paiardini, Alessandro - 01a Articolo in rivista

paper: BIOINFORMATICS ([Oxford] : Oxford University Press) pp. 1-3 - issn: 1367-4811 - wos: WOS:001101066800001 (2) - scopus: 2-s2.0-85176804397 (1)

11573/1662673 - 2022 - Severe Bartter syndrome type 1: Prompt postnatal management thanks to antenatal identification of SLC12A1 pathogenic variants

D'angelantonio, D; Majore, S; Di Netta, T; Zotta, F; Parise, G; Savino, E; Rosignoli, S; Bizzarri, B; Signore, F; Grammatico, P; Bottillo, I - 01a Articolo in rivista

paper: ARCHIVES DE PEDIATRIE (Editions Scientifique & Medical Elsevier:23 Rue Linois, F 75724 Paris Cedex 15 France:011 33 1 71724646, INTERNET: http://www.elsevier.fr, Fax: 011 33 1 71724664) pp. 530-533 - issn: 0929-693X - wos: WOS:000965565600010 (1) - scopus: 2-s2.0-85138547085 (1)

11573/1625113 - 2022 - Prediction and modeling of protein–protein interactions using “Spotted” peptides with a template-based approach

Gasbarri, C.; Rosignoli, S.; Janson, G.; Boi, D.; Paiardini, A. - 01a Articolo in rivista

paper: BIOMOLECULES (Basel: MDPI) pp. 201- - issn: 2218-273X - wos: WOS:000763712100001 (1) - scopus: 2-s2.0-85123311952 (3)

11573/1655650 - 2022 - DockingPie: a consensus docking plugin for PyMOL

Rosignoli, Serena; Paiardini, Alessandro - 01a Articolo in rivista

paper: BIOINFORMATICS (-Oxford : Oxford University Press, 1998-) pp. 4233-4234 - issn: 1367-4803 - wos: WOS:000824423300001 (17) - scopus: 2-s2.0-85141892299 (15)

11573/1661534 - 2022 - Boosting the full potential of PyMOL with structural biology plugins

Rosignoli, Serena; Paiardini, Alessandro - 01g Articolo di rassegna (Review)

paper: BIOMOLECULES (Basel: MDPI) pp. 1764- - issn: 2218-273X - wos: WOS:000902276900001 (51) - scopus: 2-s2.0-85144708388 (64)

11573/1534289 - 2021 - The archaeal elongation factor EF-2 induces the release of aIF6 from 50S ribosomal subunit

Lo Gullo, Giada; De Santis, Maria Luisa; Paiardini, Alessandro; Rosignoli, Serena; Romagnoli, Alice; La Teana, Anna; Londei, Paola; Benelli, Dario - 01a Articolo in rivista

paper: FRONTIERS IN MICROBIOLOGY (Lausanne : Frontiers Research Foundation, 2010-) pp. 631297- - issn: 1664-302X - wos: WOS:000637212200001 (3) - scopus: 2-s2.0-85103823367 (3)

11573/1600685 - 2021 - Design and development of a versatile graphical user interface for assisting consensus docking analyses on therapeutic targets for cancer treatment.

Rosignoli, Serena; Paiardini, Alessandro - 04f Poster

conference: EMBO Workshop - Systems approaches in cancer (Split; Croatia)

book: Systems approaches in cancer - ()