User:Lorenzo Pasotti: Difference between revisions

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*Lorenzo Pasotti
*Lorenzo Pasotti
*University of Pavia
*University of Pavia
*via Ferrata 3, Pavia I-27100, Italy
*via Ferrata 5, Pavia I-27100, Italy
*[[Special:Emailuser/Lorenzo Pasotti|Email me through OpenWetWare]]
*lorenzo dot pasotti at unipv dot it


I work in the Laboratory for Biomedical Informatics and in the molecular biology lab of the Centre for Tissue Engineering (see [[Your Lab]] on OWW) at the University of Pavia.
I work on synthetic biology in the Laboratory Bioinformatics, Mathematical Modelling and Synthetic Biology (BMS) and in the molecular biology lab of the Centre for Health Technologies (see [[Magni]] lab on OWW), University of Pavia.


==Education==
==Education and current position==
<!--Include info about your educational background-->
<!--Include info about your educational background-->
* 2012, PhD, University of Pavia
* 2015-, Researcher, University of Pavia
* 2008, MS, University of Pavia
* 2012-2015, Postdoc researcher, University of Pavia
* 2006, BS, University of Pavia
* Feb-Sep 2011, visiting PhD student, School of Biological Sciences, University of Edinburgh, UK
* 2008-2012, PhD, Bioengineering and Bioinformatics, University of Pavia
* 2006-2008, MS, Biomedical Informatics, University of Pavia
* 2003-2006, BS, Biomedical Engineering, University of Pavia


==Research interests==
==Research interests==
<!-- Feel free to add brief descriptions to your research interests as well -->
<!-- Feel free to add brief descriptions to your research interests as well -->
# Modularity of biological parts
# Predictability of biological parts and synthetic circuits
# Pathway engineering for biofuel production
# Metabolic engineering of pathways for biofuel and biopolymer production
# Bottom-up design and modelling of gene networks
# Bottom-up design and modelling of gene networks
# Quorum sensing re-engineering


==Publications==
==Publications==
<!-- Replace the PubMed ID's ("pmid=#######") below with the PubMed ID's for your publications.  You can add or remove lines as needed -->
<!-- Replace the PubMed ID's ("pmid=#######") below with the PubMed ID's for your publications.  You can add or remove lines as needed -->
#Bandiera L, Pasini A, Pasotti L, Zucca S, Mazzini G, Magni P, Giordano E, Furini S (2016) Experimental measurements and mathematical modeling of biological noise arising from transcriptional and translational regulation of basic synthetic gene circuits. ''Journal of Theoretical Biology'', 395:153-60. [http://www.sciencedirect.com/science/article/pii/S0022519316000941 Link]
#Casanova M, Pasotti L, Zucca S, Politi N, Massaiu I, Calvio C, Cusella De Angelis MG, Magni P (2016) A BioBrickTM-compatible vector for allelic replacement using the xylE gene as selection marker. ''Biological Procedures Online'', 18:6. [http://biologicalproceduresonline.biomedcentral.com/articles/10.1186/s12575-016-0036-z Link]
#Massaiu I, Pasotti L, Casanova M, Politi N, Zucca S, Cusella De Angelis MG, Magni P (2015) Quantification of the gene silencing performances of rationally-designed synthetic small RNAs. ''Systems and Synthetic Biology'', 9(3):107-23. [http://link.springer.com/article/10.1007%2Fs11693-015-9177-7 Link]
#Pasotti L, Zucca S, Casanova M, Politi N, Massaiu I, Mazzini G, Micoli G, Calvio C, Cusella De Angelis MG, Magni P (2015) Methods for genetic optimization of biocatalysts for biofuel production from dairy waste through synthetic biology. ''IEEE EMBC proceedings'', Milano, Italy, August 25-29.
#Swat MJ, Moodie S, Wimalaratne SM, Kristensen NR, Lavielle M, Mari A, Magni P, Smith MK, Bizzotto R, Pasotti L et al. (2015) Pharmacometrics Markup Language (PharmML): opening new perspectives for model exchange in drug development. ''CPT Pharmacometrics and Systems Pharmacology'', 4(6):316–319. [http://onlinelibrary.wiley.com/doi/10.1002/psp4.57/full Link]
#Zucca S, Pasotti L, Politi N, Casanova M, Mazzini G, Cusella De Angelis MG, Magni P (2015) Multi-faceted characterization of a novel LuxR-repressible promoter library for ''Escherichia coli''. ''PLoS ONE'', 10(5):e0126264. [http://www.plosone.org/article/authors/info%3Adoi%2F10.1371%2Fjournal.pone.0126264 Link]
#Politi N, Pasotti L, Zucca S, Magni P (2015) Modelling the effects of cell-to-cell variability on the output of interconnected gene networks in bacterial populations. ''BMC Systems Biology'', 9(Suppl 3):S6. [http://www.biomedcentral.com/1752-0509/9/S3/S6 Link]
#Tiengo A, Pasotti L, Barbarini N, Magni P (2015) PhosphoHunter: An efficient software tool for phosphopeptide identification. ''Advances in Bioinformatics'', Article ID: 382869. [http://www.hindawi.com/journals/abi/2015/382869/ Link]
#Pasotti L, Zucca S (2014) Advances and computational tools towards predictable design in biological engineering. ''Computational and Mathematical Methods in Medicine'', Article ID: 369681. [http://www.hindawi.com/journals/cmmm/2014/369681/ Link]
#Politi N, Pasotti L, Zucca S, Casanova M, Micoli G, Cusella De Angelis MG, Magni P (2014) Half-life measurements of chemical inducers for recombinant gene expression. ''Journal of Biological Engineering'', 8:5. [http://www.jbioleng.org/content/8/1/5 Link]
#Pasotti L, Zucca S, Magni P (2013) Modelling for synthetic biology. Book chapter in: ''Modeling Methodology for Physiology and Medicine: Second Edition'' (Elsevier), p.545-564. DOI: 10.1016/B978-0-12-411557-6.00023-9.
#Zucca S, Pasotti L, Politi N, Cusella De Angelis MG, Magni P (2013) A standard vector for the chromosomal integration and characterization of BioBrickTM parts in ''Escherichia coli''. ''Journal of Biological Engineering'', 7:12. [http://www.jbioleng.org/content/7/1/12 Link]
#Pasotti L, Politi N, Zucca S, Cusella De Angelis MG, Magni P (2012) Bottom-up engineering of biological systems through standard bricks: A modularity study on basic parts and devices. ''PLoS ONE'', 7(7). [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039407 Link]
#Zucca S, Pasotti L, Mazzini G, Cusella De Angelis MG, Magni P (2012) Characterization of an inducible promoter in different DNA copy number conditions. ''BMC Bioinformatics'', 13(Suppl 4): S11. [http://www.biomedcentral.com/1471-2105/13/S4/S11 Link]
#Zucca S, Pasotti L, Mazzini G, Cusella De Angelis MG, Magni P (2012) Characterization of an inducible promoter in different DNA copy number conditions. ''BMC Bioinformatics'', 13(Suppl 4): S11. [http://www.biomedcentral.com/1471-2105/13/S4/S11 Link]
#Pasotti L, Quattrocelli M, Galli D, De Angelis MG, Magni P (2011) Multiplexing and demultiplexing logic functions for computing signal processing tasks in synthetic biology. ''Biotechnology Journal'', 6(7):784-95. [http://onlinelibrary.wiley.com/doi/10.1002/biot.201100080/abstract Link]
#Pasotti L, Quattrocelli M, Galli D, De Angelis MG, Magni P (2011) Multiplexing and demultiplexing logic functions for computing signal processing tasks in synthetic biology. ''Biotechnology Journal'', 6(7):784-95. [http://onlinelibrary.wiley.com/doi/10.1002/biot.201100080/abstract Link]
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*[[Help|OpenWetWare help pages]]
*[[Help|OpenWetWare help pages]]
*[http://partsregistry.org/ Registry of Standard Biological Parts]
*[http://partsregistry.org/ Registry of Standard Biological Parts]
*[http://web.expasy.org/translate/ ExPASy Translate tool]
*[http://web.expasy.org/translate/ ExPASy Translate Tool]
*[http://www.bioinformatics.org/sms/rev_comp.html Reverse Complement]
*[http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi RNAfold web server]
*[http://blast.ncbi.nlm.nih.gov/ BLAST]
*[http://mfold.rna.albany.edu/ UNAFold web server]
*[https://salis.psu.edu/software/ RBS Calculator]
*[http://cgsc.biology.yale.edu/ Coli Genetic Stock Center]
*[http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi RNAfold web server (useful for secondary structure determination)]
*[http://openwetware.org/wiki/E._coli_genotypes ''E. coli'' genotypes]
*[http://mfold.rna.albany.edu/ UNAFold web server (useful for hybridization and folding energy determination)]
*[http://cgsc.biology.yale.edu/ Coli Genetic Stock Center at Yale University]

Revision as of 03:24, 4 December 2016

Contact Info

Lorenzo Pasotti
  • Lorenzo Pasotti
  • University of Pavia
  • via Ferrata 5, Pavia I-27100, Italy
  • lorenzo dot pasotti at unipv dot it

I work on synthetic biology in the Laboratory Bioinformatics, Mathematical Modelling and Synthetic Biology (BMS) and in the molecular biology lab of the Centre for Health Technologies (see Magni lab on OWW), University of Pavia.

Education and current position

  • 2015-, Researcher, University of Pavia
  • 2012-2015, Postdoc researcher, University of Pavia
  • Feb-Sep 2011, visiting PhD student, School of Biological Sciences, University of Edinburgh, UK
  • 2008-2012, PhD, Bioengineering and Bioinformatics, University of Pavia
  • 2006-2008, MS, Biomedical Informatics, University of Pavia
  • 2003-2006, BS, Biomedical Engineering, University of Pavia

Research interests

  1. Predictability of biological parts and synthetic circuits
  2. Metabolic engineering of pathways for biofuel and biopolymer production
  3. Bottom-up design and modelling of gene networks
  4. Quorum sensing re-engineering

Publications

  1. Bandiera L, Pasini A, Pasotti L, Zucca S, Mazzini G, Magni P, Giordano E, Furini S (2016) Experimental measurements and mathematical modeling of biological noise arising from transcriptional and translational regulation of basic synthetic gene circuits. Journal of Theoretical Biology, 395:153-60. Link
  2. Casanova M, Pasotti L, Zucca S, Politi N, Massaiu I, Calvio C, Cusella De Angelis MG, Magni P (2016) A BioBrickTM-compatible vector for allelic replacement using the xylE gene as selection marker. Biological Procedures Online, 18:6. Link
  3. Massaiu I, Pasotti L, Casanova M, Politi N, Zucca S, Cusella De Angelis MG, Magni P (2015) Quantification of the gene silencing performances of rationally-designed synthetic small RNAs. Systems and Synthetic Biology, 9(3):107-23. Link
  4. Pasotti L, Zucca S, Casanova M, Politi N, Massaiu I, Mazzini G, Micoli G, Calvio C, Cusella De Angelis MG, Magni P (2015) Methods for genetic optimization of biocatalysts for biofuel production from dairy waste through synthetic biology. IEEE EMBC proceedings, Milano, Italy, August 25-29.
  5. Swat MJ, Moodie S, Wimalaratne SM, Kristensen NR, Lavielle M, Mari A, Magni P, Smith MK, Bizzotto R, Pasotti L et al. (2015) Pharmacometrics Markup Language (PharmML): opening new perspectives for model exchange in drug development. CPT Pharmacometrics and Systems Pharmacology, 4(6):316–319. Link
  6. Zucca S, Pasotti L, Politi N, Casanova M, Mazzini G, Cusella De Angelis MG, Magni P (2015) Multi-faceted characterization of a novel LuxR-repressible promoter library for Escherichia coli. PLoS ONE, 10(5):e0126264. Link
  7. Politi N, Pasotti L, Zucca S, Magni P (2015) Modelling the effects of cell-to-cell variability on the output of interconnected gene networks in bacterial populations. BMC Systems Biology, 9(Suppl 3):S6. Link
  8. Tiengo A, Pasotti L, Barbarini N, Magni P (2015) PhosphoHunter: An efficient software tool for phosphopeptide identification. Advances in Bioinformatics, Article ID: 382869. Link
  9. Pasotti L, Zucca S (2014) Advances and computational tools towards predictable design in biological engineering. Computational and Mathematical Methods in Medicine, Article ID: 369681. Link
  10. Politi N, Pasotti L, Zucca S, Casanova M, Micoli G, Cusella De Angelis MG, Magni P (2014) Half-life measurements of chemical inducers for recombinant gene expression. Journal of Biological Engineering, 8:5. Link
  11. Pasotti L, Zucca S, Magni P (2013) Modelling for synthetic biology. Book chapter in: Modeling Methodology for Physiology and Medicine: Second Edition (Elsevier), p.545-564. DOI: 10.1016/B978-0-12-411557-6.00023-9.
  12. Zucca S, Pasotti L, Politi N, Cusella De Angelis MG, Magni P (2013) A standard vector for the chromosomal integration and characterization of BioBrickTM parts in Escherichia coli. Journal of Biological Engineering, 7:12. Link
  13. Pasotti L, Politi N, Zucca S, Cusella De Angelis MG, Magni P (2012) Bottom-up engineering of biological systems through standard bricks: A modularity study on basic parts and devices. PLoS ONE, 7(7). Link
  14. Zucca S, Pasotti L, Mazzini G, Cusella De Angelis MG, Magni P (2012) Characterization of an inducible promoter in different DNA copy number conditions. BMC Bioinformatics, 13(Suppl 4): S11. Link
  15. Pasotti L, Quattrocelli M, Galli D, De Angelis MG, Magni P (2011) Multiplexing and demultiplexing logic functions for computing signal processing tasks in synthetic biology. Biotechnology Journal, 6(7):784-95. Link
  16. Pasotti L, Zucca S, Lupotto M, Cusella De Angelis MG, Magni P (2011) Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins release. Journal of Biological Engineering, 5:8. Link

Useful links

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