Monica Maria Zoppe'
Research staff
Monica Zoppè studied in Milan and continued her research career in several laboratories in Italy and abroad, including the University of Birmingham, UK, the Salk Institute of La Jolla, USA, ICGEB in Trieste, and IFC in Pisa. After many years of ‘wet research’, since 2007, she started a project aimed at the elaboration, interpretation and visualization of biological processes using the techniques developed for Computer Graphics, animation and gaming. Between 2007 and 2014 we created and used BioBlender, a specific AddOn for biological work in Blender, based on the assumption that we humans have a special ability at grasping information presented visually, and easily recognize patterns and identify exceptions after only a few sights of new phenomena. The SciVis website presents some of the videos.
After moving to Milano, Monica’s work has been dedicated to other aspects of representations: a theoretical study of colors and signs, and a method for the preparation of tangible models of proteins either in hard plastic (3D-printed), or in soft rubber.
orcid://0000-0003-4590-0718,
Contact:
- Email monica.zoppe@cnr.it
- Phone +39-02-23699547
- Location Milano
Website:
Research interests:
- SciVis (Principal investigator)
- Rubber proteins (Principal investigator)
- ProQuaB (Principal investigator)
Further collaborations:
- Claudia Caudai, ISTI CNR, (Pisa)
- Emanuele Salerno , ISTI CNR, (Pisa)
- Maria Antonietta Pascali, ISTI CNR, (Pisa)
- Daniela Giorgi, ISTI CNR, (Pisa)
- Thomas Alderighi, ISTI CNR, (Pisa)
- Edisel Navas, Univesidad de Ciencias Informaticas, (La Havana, Cuba)
- Pablo E. Ramos Univesidad de Ciencias Informaticas, (La Havana, Cuba)
- Tiziana Loni, Independent artist (Glasgow, UK)
Key publications:
Zoppè, M. Colors in the representation of biological structures. Journal of Integrative Bioinformatics (JIB). 2022 Jul 4;19(2):20220021.
Alderighi T, Giorgi D, Malomo L, Cignoni P, Zoppè M. Computational design, fabrication and evaluation of rubber protein models. Computers & Graphics. 2021 Jun;S0097849321001096.
Zoppè M. Improving Gender Diversity in Science. In: #WeTooInScience - Sexual Harassment in Higher Education Institutions and Research Organizations. Rome, Italy: CNR-IRPPS e-Publishing; 2019. p. 235–41.
Caudai C, Salerno E, Zoppè M, Tonazzini A. Estimation of the Spatial Chromatin Structure Based on a Multiresolution Bead-Chain Model. IEEE/ACM transactions on computational biology and bioinformatics [Internet]. 2018 Jan 9; Available from: http://www.ncbi.nlm.nih.gov/pubmed/29994172
Zoppè M, Loni T. The Representation of Electrostatics for Biological Molecules. In: Rocchia W, Spagnuolo M, editors. Computational Electrostatics for Biological Applications: Geometric and Numerical Approaches to the Description of Electrostatic Interaction Between Macromolecules. Cham: Springer International Publishing; 2015. p. 215–25.
Publications (33):
High-level biocontainment laboratories: risks and necessity for societyZoppè, Monica
F1000, 2022
DOI: 10.12688/f1000research.111073.1
Virucidal Activity of the Pyridobenzothiazolone Derivative HeE1-17Y against Enveloped RNA Viruses
Bonotto R.M.; Boni F.; Milani M.; Chaves-Sanjuan A.; Franze S.; Selmin F.; Felicetti T.; Bolognesi M.; Konstantinidou S.; Poggianella M.; Marquez C.L.; Dattola F.; Zoppe M.; Manfroni G.; Mastrangelo E.; Marcello A.
Viruses, 2022
DOI: 10.3390/v14061157
Colors in the representation of biological structures
Zoppe M.
Journal of integrative bioinformatics, 2022
DOI: 10.1515/jib-2022-0021
Integration of multiple resolution data in 3D chromatin reconstruction using ChromStruct
Caudai C.; Zoppè M.; Tonazzini A.; Merelli I.; Salerno E.
Biology (Basel), 2021
DOI: 10.3390/biology10040338
Computational design, fabrication and evaluation of rubber protein models
Alderighi T.; Giorgi D.; Malomo L.; Cignoni P.; Zoppè M.
Computers & graphics, 2021
DOI: 10.1016/j.cag.2021.05.010
Estimation of the spatial chromatin structure based on a multiresolution bead-chain model
Caudai C.; Salerno E.; Zoppe M.; Tonazzini A.
IEEE/ACM transactions on computational biology and bioinformatics (Print), 2019
DOI: 10.1109/TCBB.2018.2791439
ChromStruct 4: a Python code to estimate the chromatin structure from Hi-C data
Caudai C.; Salerno E.; Zoppè M.; Merelli I.; Tonazzini A.
IEEE/ACM transactions on computational biology and bioinformatics (Online), 2019
DOI: 10.1109/TCBB.2018.2838669
Making of The Dark Anim Technical and scientific notes
Loni, Tiziana; Carlone, Ilaria; Cianchetta, Stefano; Zoppe, Monica
ieee xplore digital library, 2019
DOI: 10.1109/CW.2019.00016
Towards a perceptive understanding of size in cellular biology
Zoppe, Monica
Nature methods, 2017
DOI: 10.1038/nmeth.4300
Inferring 3D chromatin structure using a multiscale approach based on quaternions
Caudai C.; Salerno E.; Zoppè M.; Tonazzini A.
BMC bioinformatics, 2015
DOI: 10.1186/s12859-015-0667-0
Comunicare l'invisibile. La rappresentazione visiva di concetti biofisici
Monica Zoppè
Progetto grafico, 2014
Myocardial contractility in the stress echo lab: from pathophysiological toy to clinical tool
Bombardini T, Zoppè M, Ciampi Q, Cortigiani L, Agricola E, Salvadori S, Loni T, Pratali L, Picano E
Cardiovascular ultrasound, 2013
DOI: 10.1186/1476-7120-11-41
Intuitive representation of surface properties of biomolecules using BioBlender
Andrei R. M.; Callieri M.; Zini M.F.; Loni T.; Maraziti G.; Pan M.C.; Zoppè M.
BMC bioinformatics, 2012
DOI: 10.1186/1471-2105-13-S4-S16
Step back form the edge
Monica Zoppè
EMBO reports (Print), 2012
DOI: 10.1038/embor.2012.123
Vedere l'invisibile
Monica Zoppè
Le Scienze (Milano), 2011
Using Blender for molecular animation and scientific representation
Zoppè Monica , Yuri Porozov, Raluca Andrei, Stefano Cianchetta, Maria Francesca Zini, Tiziana Loni, Claudia Caudai, Marco Callieri
Potentiation of gene targeting in human cells by expression of Saccharomyces cerevisiae Rad52
Di Primio G.; Galli A.; Cervelli T.; Zoppè M.; Rainaldi G.
Nucleic acids research (Online), 2005
DOI: 10.1093/nar/gki778
Ribozyme-mediated inhibition of survivin expression increases spontaneous and drug-induced apoptosis and decreases the tumorigenic potential of human prostate cancer cells
Pennati, M; Binda, M; Colella, G; Zoppe', M; Folini, M; Vignati, S; Valentini, A; Citti, L; De Cesare, M; Pratesi, G; Giacca, M; Daidone, MG; Zaffaroni, N
Oncogene (Basingstoke), 2004
DOI: 10.1038/sj.onc.1207071
The human cytomegalovirus UL45 gene product is a late, virion-associated protein and influences virus growth at low multiplicities of infection.
Patrone M, Percivalle E, Secchi M, Fiorina L, Pedrali-Noy G, Zoppe M, Baldanti F, Hahn G, Koszinowski UH, Milanesi G, Gallina A.
Journal of general virology (Print), 2003
DOI: 10.1099/vir.0.19452-0
Transcellular transfer of active HSV-1 thymidine kinase mediated by an 11-amino-acid peptide from HIV-1 Tat
Tasciotti E., Zoppè M., Giacca M.
Cancer gene therapy, 2003
Cell Membrane Lipid Rafts Mediate Caveolar Endocytosis of HIV-1 Tat Fusion Proteins
Fittipaldi, A., Ferrari, A., Zoppè, M., Arcangeli, C., Pellegrini, V., Beltram, F. Giacca, M.
Multiple modes of transcriptional regulation by the HIV-1 tat transactivator
Marcello, A; Zoppe, M; Giacca, M
IUBMB life (Print), 2001
DOI: 10.1080/152165401753544241
In vitro and in vivo antisense-mediated growth inhibition of a mammary adenocarcinoma from MMTV-neu transgenic mice
Sacco, Maria Grazia; Barbieri, Ottavia; Piccini, Daniele; Noviello, Elvira; Zoppè, Monica M.; Zucchi, Ileana; Frattini, Annalisa; Villa, Anna; Vezzoni, Paolo
Gene therapy (Basingstoke), 1998
A factor IX-deficient mouse model for hemophilia B gene therapy
Wang, LL; Zoppe, M; Hackeng, TM; Griffin, JH; Lee, KF; Verma, IM
Proceedings of the National Academy of Sciences of the United States of America, 1997
DOI: 10.1073/pnas.94.21.11563
The complete sequence of the Host Cell Factor 1 (HCFC1) gene and its promoter: A role for YY1 transcription factor in the regulation of its expression
Zoppe M.; Frattini A.; Faranda S.; Vezzoni P.
Genomics (S. Diego Calif.), 1996
DOI: 10.1006/geno.1996.0244
GENERATION OF TARGETED RETROVIRAL VECTORS BY USING SINGLE-CHAIN VARIABLE FRAGMENT - AN APPROACH TO IN-VIVO GENE DELIVERY
SOMIA, NV; ZOPPE, M; VERMA, IM
Proceedings of the National Academy of Sciences of the United States of America, 1995
DOI: 10.1073/pnas.92.16.7570
Mapping of two genes encoding isoforms of the actin binding protein ABP-280, a dystrophin like protein, to Xq28 and to chromosome 7
Maestrini, Elena; Patrosso, Cristina M.; Mancini, Mita; Rivella, S.; Rocchi, Mariano; Repetto, Monica; Villa, Anna Maria; Frattini, Annalisa; Zoppè, Monica M.; Vezzoni, Paolo; Toniolo, Daniela
Human molecular genetics (Print), 1993
ZNF75 - ISOLATION OF A CDNA CLONE OF THE KRAB ZINC-FINGER GENE SUBFAMILY MAPPED IN YACS 1 MB TELOMERIC OF HPRT
VILLA, A; ZUCCHI, I; PILIA, G; STRINA, D; SUSANI, L; MORALI, F; PATROSSO, C; FRATTINI, A; LUCCHINI, F; REPETTO, M; SACCO, MG; ZOPPE, M; VEZZONI, P
Genomics (S. Diego Calif.), 1993
DOI: 10.1006/geno.1993.1459
Expression of the wild-type and mutated vacuolar storage protein phaseolin in Xenopus oocytes reveals relationships between assembly and intracellular transport
A. Ceriotti, E. Pedrazzini, M.S. Fabbrini, M. Zoppè, R. Bollini, A. Vitale
European journal of biochemistry (Print), 1991
DOI: 10.1111/j.1432-1033.1991.tb16456.x
MANNOSE ANALOG 1 DEOXYMANNOJIRIMYCIN INHIBITS THE GOLGI-MEDIATED PROCESSING OF BEAN STORAGE GLYCOPROTEINS
VITALE A; ZOPPE M; BOLLINI R
Plant physiology (Bethesda), 1989
DOI: 10.1104/pp.89.4.1079
SYNTHESIS OF LECTIN-LIKE PROTEIN IN DEVELOPING COTYLEDONS OF NORMAL AND PHYTOHEMAGGLUTININ-DEFICIENT PHASEOLUS-VULGARIS
VITALE A; ZOPPE M; FABBRINI M S; GENGA A; RIVAS L; BOLLINI R
Plant physiology (Bethesda), 1989
DOI: 10.1104/pp.90.3.1015
Synthesis of Lectin-like Protein in developing Bean Cotyledons of normal and Phytohemagglutinin-deficient
Vitale, A. Zoppè, M., Fabbrini, M.S., Genga, A.M., Rivas, L. and Bollini, R.
Plant physiology (Online), 1989
1-Deoxymannojirimycin inhibits Golgi-mediated processing of glycoprotein in Xenopus oocytes
Fabbrini, Maria Serena; Zoppè, Monica; Bollini, Roberto; Vitale, Alessandro
FEBS letters (Print), 1988
DOI: 10.1016/0014-5793(88)80144-3