Publications (in alphabetical and chronological order)

PAPERS

  • Vaggi F, Dodgson J, Bajpai A, Chessel A, Jordan F, Sato M, Carazo-Salas RE, Csikasz-Nagy A, Linkers of cell polarity and cell cycleregulation in the fission yeast protein interaction network, PLoS Computational Biology 2012 8(10): e1002732  link
  • Dassi E., Quattrone A., "Tuning the engine: an introduction to resources on post-transcriptional regulation of gene expression". RNA Biology, 9 (10), 2012
  •  E. Dassi; A. Malossini; A. Re; T. Mazza; T. Tebaldi; L. Caputi; A. Quattrone, AURA: Atlas of UTR Regulatory Activity, Bioinformatics 2011; doi: 10.1093/bioinformatics/btr608  link
  • I. Djinni, A. Defant, M. Kecha, I. Mancini, ″Antibacterial Polyketides from the Marine Alga-Derived Endophitic Streptomyces sundarbansensis. A Study on Hydroxypyrone Tautomerism. Marine Drugs,  special issue: Marine Antibiotics. Accepted
  • V. F. Tamboli, N. Re, C. Coletti, A. Defant, I. Mancini, P. Tosi, ″A joint experimental and theoretical investigation on the oxidative coupling of resveratrol induced by copper and iron ions″, International Journal of Mass Spectrometry, 2012, 319-320, 55-63G.
  • Cazzolli, S. Caponi, A. Defant,  C. M. C. Gambi, S. Marchetti, M. Mattarelli, M. Montagna,  B. Rossi,  F. Rossia and G. Viliani, ″Aggregation processes in micellar solutions: a Raman study″, Journal of  Raman Spectroscopy,  DOI 10.1002/jrs.4120
  • L. Chiari, A. Zecca, S. Girardi, A. Defant, F. Wang, X. G. Ma, M. V. Perkins, and M. J. Brunger, ″Positron scattering from chiral enantiomers″, Physical Review A,  2012, 85, 052711
  • A. Zovko , M. Vaukner Gabric , K. Sepcic , F. Pohleven , D. Jaklic, N. Gunde-Cimerman , Z. Lu , R.A. Edrada-Ebel , W. E. Houssen , I. Mancini, A. Defant , M. Jaspars, T. Turk, ″Antifungal and antibacterial activity of 3-alkylpyridinium polymeric analogs of marine toxins″, International Biodeterioration & Biodegradation, 2012, 68, 71-77
  • Vajir Tamboli, Andrea Defant, Ines Mancini, Paolo Tosi, "A study of resveratrol-copper complexes by electrospray ionization mass spectrometry and density functional theory calculations"  in Rapid Communications in Mass Spectrometry, v. 25, (2011), p. 526-532. - DOI: 10.1002/rcm.4883
  • I.Mancini, A. Defant, T. Mesaric, F. Potocnik, U. Batista, G. Guella, T. Turk, K. Sepcic, "Fatty acid composition of common barbel ( Barbusbarbus) roe and evaluation of its haemolytic and cytotoxic activities" in TOXICON, v. 2011/57, n. 7 (2011), p. 1017-1022. - DOI: 10.1016/j.toxicon.2011.04.004
  • A. Defant, I.Mancini, L. Raspor, G. Guella, T. Turk, K. Sepcic, "New structural insights into saraines A, B and C, macrocyclic alkaloids from the mediterranean sponge Reniera (Haliclona) sarai" in EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, v. 2011/20,21, (2011), p. 3761-3767. - DOI: 10.1002/ejoc.201100434. - Special Issue: Women in Chemistry
  • A. Defant, I.Mancini, C. Torri, D. Malferrari, D. Fabbri, "An efficient route towards a new branched tetrahydrofurane delta-sugar amino acid from a pyrolysis product of cellulose" in Amino Acids, v. 2010, (2010), p. 1-8. - DOI: 10.1007/s00726
  • A. Defant, B. Rossi, G. Viliani, G. Guella, I. Mancini, "Metal-assisted regioselectivity in nucleophilic substitutions: a study by Raman spectroscopy and density functional theory calculations" in Journal of Raman Spectroscopy, v. 2010, (2010), p. 1-6. - DOI: 10.1002/jrs.2631
  • P. Franceschi, Y. Dong, K. Strupat, U. Vhrovsek, F. Mattivi, "Combining intensity correlation analysis and MALDI imaging to study the distribution of flavonoid glycosides in Golden Delicious apples". J. Exp Bot. 2011 Nov 25. [Epub ahead of print]  DOI:10.1093/jxb/err327
  • A. Barla, G. Jurman, R. Visintainer, M. Squillario, M. Filosi, S. Riccadonna, C. Furlanello, "A Machine Learning Pipeline for Discriminant Pathway Identification", Springer Handbook of Bio-and Neurosicence, LNBI/LNCS Series, Springer in Press 2012
  • D. Albanese*, M. Filosi*, R. Visintainer*, S. Riccadonna, G. Jurman, C. Furlanello, "Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers", Bioinformatics, 2012
  • Tuohy KM, Conterno L, Gasperotti M,  Viola R, "Up-regulating the Human Intestinal Microbiome Using Whole Plant Food, Polyphenols, and/or Fiber", Journal of Agricultural and Food Chemistry, 2012, 60, 36, SI, pp. 8776-8782 (DOI: 10.1021/jf2053959)
  • Vhrovsek U., Masuero D., Gasperotti M., Franceschi P., Caputi L., Viola R., Mattivi F., "A versatile targeted metabolomics method for the rapid quantification of multiple classes of phenolics in fruits and beverages", Journal of Agricultural and Food Chemistry, 2012, 60, 36SI, pp. 8831-8840 (DOI: 10.1021/Jf2051569)
  • Fedrizzi B., Guella G., Perenzoni D., Gasperotti M., Masuero D., Vhrovsek U., Mattivi F., "Identification of intermediates involved in the biosynthetic pathway of 3-mercaptohexan-1-ol conjugates in yellow passion fruit (Passiflora edulis f. flavicarpa)", Phytochemistry, 2012, 77, pp. 287-293 (DOI:10.1016/j.phytochem.2012.01.017)
  • Vhrovsek U., Guella G., Gasperotti M., Pojer E., Zancato M., Mattivi F., "Clarifying the identity of the main Ellagitannin in the fruit of the strawberry, Fragaria vesca and Fragaria ananassa Duch.", Journal of Agricultural and Food Chemistry, 2012, 60, 10, pp. 2507-2516 (DOI: 10.1021/jf2052256)
  • Vanzo A., Scholz M., Gasperotti M., Tramer F., Passamonti S., Vhrovsek U., Mattivi F., "Metabolomic investigation of rat tissues following intravenous administration of cyanidin 3-glucoside at a physiologically relevant dose", Metabolomics, 2012 (DOI: 10.1007/s11306-012-0430-8)
  • Forlin M., Lentini R., Mansy S.S., "Cellular Imitations". 2012, Curr Opin Chem Biol, 16,586-592 link

  • Andreotti V, Ciribilli Y, Monti P, Bisio A, Lion M, et al. 2011. "p53 Transactivation and the Impact of Mutations, Cofactors and Small Molecules Using a Simplified Yeast-Based Screening System". PLoS ONE 6(6): e20643. doi:10.1371/journal.pone.0020643 link

  • C. Potrich, L. Lunelli, L. Pasquardini, D. Sonn, D. Vozzi, R. Dallapiccola, L. Marocchi, I. Ferrante, O. Rossotto, C. Pederzolli. One-shot genetic analysis in monolithic Silicon/Pyrex microdevices. Biomedical Microdevices 257 (2011), pp. 10821-10827 DOI 10.007/s10544-012-9676-1  link

  • L. Pasquardini, L. Lunelli, C. Potrich, L. Marocchi, S. Fiorilli, D. Vozzi, L. Vanzetti, P. Gasparini, M. Anderle, C. Pederzolli, Organo-silane coated substrates for DNA purification. Applied Surface Science 257 (2011), pp. 10821-10827  link

  • Torino D., Martini L., Mansy S. S., "Piecing together cell-like systems", Curr. Org. Chem, in press

  • Laura Martini and Sheref Mansy, Cell-like systems with riboswitch controlled gene expression. Chem. Commun., 2011, 47, 10734-10736. DOI: 10.1039/C1CC13930D  link

  • Vidalino L., Monti L., Haase A., Moro A., Acquati F., Taramelli R., Macchi P. "Intracellular trakkicking of RNASET2, a novel component of P-bodies". Biol Cell. 2012 Jan; 104(1):13-21. doi:10.111/boc.201100092.Epub 2011 Dec 1. link

  • Janjua Ha, N. Segata, P. Bernabò, S. Tamburini, A. Ellen, O. Jousson, "Clinical populations of Pseudomonas aeruginosa isolated from acute infections show a high virulence range partially correlated with population structure and virulence gene expression" in MICROBIOLOGY, v. 158, (2012), p. 2089-2098   link

  • Tremaroli V, Fedi S, Tamburini S, Viti C, Tatti E, Ceri H, Turner RJ, Zannoni D. A histidine-kinase cheA gene of Pseudomonas pseudoalcaligens KF707 not only has a key role in chemotaxis but also affects biofilm formation and cell metabolism. Biofouling. 2011 Jan;27(1):33-46.

  • Foladori P., Tamburini S., Bruni L. (2010) Bacterial permeabilisation and disruption caused by sludge reduction technologies evaluated by flow cytometry. Water Res. 2010 Sep;44(17):4888-99. Epub 2010 Jul 16.
  • Foladori P., Bruni L., Tamburini S., Ziglio G. (2010) Direct quantification of bacterial biomass in influent, effluent and activated sludge of  wastewater treatment plants by usingflow cytometry. Water Res. 2010 Jul;44(13):3807-18. Epub 2010 Apr 29.
  • Provenzano G., Zunino G., Genovesi S., Sgadò P., Bozzi Y., Mutant mouse models of autism spectrum disorders, Dis Markers. 2012 Jan 1;33(5):225-39. doi: 10.3233/DMA-2012-0917. link

 

BOOK CHAPTERS

  • Barla, G.Jurman, R.Visintainer, M. Squillario, M.Filosi, S. Riccadonna and C. Furlanello. A machine learning pipeline for discriminant pathways identification: a systems biology approach. Editor: N. Kasabov. Springer Handbook of Bio-and Neuroinformatics (to appear, 2012)
  • I. Mancini and A.Defant, Bioactive poly(arsenic) compounds, contribution after invite to I.M. for the "Progress in Molecular and Subcellular Biology "book series, editor H. C. Schröder, Springer Verlag. In press

 

ABSTRACTS

  • N. Bacchi, G. Covello, F. Fontana, K. Siva, V. Del Vescovo, T. Incitti, A. Messina, S. Casarosa, M.A. Denti. RNA-mediated gene therapy of retinal dystrophies and dysfunctions. Joint national PhD meeting, 20-22 Octover 2011
  • Bajpai A, Vaggi F, Jordan F, Csikasz-Nagy A, "Computational analysis of the cell growth regulatory network of fission teast cells, th European conference on Mathematical and Theoretical Biology, Krakow Poland, June 28-July 2, 2011
  • Vaggi F, Bajpai A, Carazo-Salas RE, Sato M, Csikasz-Nagy A, "Finding key regulators of fission yeast polarizede growth by network analysis, 2011
  • Marina Alamanou, Elisa Latorre, Ilaria Castiglioni, Toma Tebaldi, Alessandra Bisio, Alberto Inga, Alessandro Quattrone, Alessandro Provenzani. HuR mediates a broad translational control program by a sequence-dependent mechanism during the early phase of estrogen response in MCF-7 cells
  • Clamer M, "Single molecule RNA detection through a chimeric nanopore" enGENEious 2012 conference, Christ Church, Oxford, 25-26 June 2012

  • Clamer M, Tebaldi T, Dassi E, Dalla Serra M, Quattrone A and Viero G."Hijacking of gene expression by membrane-dependent translational tuning: a system perspective", EMBL ACT, Heidelberg, Germany, 7-11 September 2011)

  • Clamer M., Dalla Serra M, Quattrone A. and Viero G. "Translational tuning by bacterial pore forming toxin on Neuroblastoma". National Congress of SIBPA (Italian Society of Pure and Applied Biophysics (Arcidosso, Grosseto, 2010)

  • Dassi E, Tebaldi T, Zuccotti P, Riva P, Quattrone A. "A translational network of rna binding proteins derived from the identification of phylogenetic footprints in 3' untranslated regions" FEBS-SystemsX-SysBio2011: From Molecules To Function, Innsbruck, Austria, Feb 26-March 4 2011
  • Dassi E., Tebaldi T., Zuccotti P., Riva P., Quattrone A. "An extended translational network involving transcription factors and RNA binding proteins derived from the identification of phylogenetic footprints in 5’ and 3’ untranslated regions".  ECCB10, 9th European Conference on computational Biology (Ghent, Belgium, 2010)
  • Angela Re, Erik Dassi, Viktoryia Sidarovich, Toma Tebaldi, Paola Scaruffi, Gian Paolo Tonini, Alessandro Quattrone. Identifying lesions in translational control of gene expression in neuroblastoma by mRNA polysomal profiling and information-intensive computational integration. ANR 2010 –Advances in Neuroblastoma Research (Stockholm, Sweden, 2010)
  • Andrea Defant and Ines Mancini″ A study on the regioselectivity in N, C-acylation of β-enamino esters″ 16th International Electronic Conference on Synthetic Organic Chemistry. 1-30 November  2012.
  • Andrea Defant and Ines Mancini “Numeric Simulation on Biological Macromolecules Applied to Drug Design: Molecular Docking in the Study of New Potential Anti-HIV
    Agents”. Andalo (Trento), Italy, March 18th - 22nd  2012
  • Vajir Tamboli, Ines Mancini, Andrea Defant, PaoloTosi. "An ESI-MS/MS study on metal ion-catalyzed oxidative dimerization of resveratrol and its synthetic analogues. 29th IMMS, Fiera di Primiero, Italy, May 2011
  • Vajir Tamboli, Ines Mancini, Andrea Defant, PaoloTosi. "An ESI-MS/MS study on copper complexes of resveratrol and its dihydrofuran dimmer". La Spettrometria di massa nello studio delle biomolecole, Bari, Italy, November 2010. 
  • Andrea Defant, Alessandro Poli and Ines Mancini. "New antitumoral molecules and DNA interactions: a study by docking calculations supporting spectroscopic evidences and biological activities". E-WiSPOC- European Winter School on Physical Organic Chemistry 2010, Bressanone, Italy, 31 January-5 February 2010.
  • G. Jurman, M. Filosi, R. Visintainer, S. Riccadonna, C. Furlanello, "Stability Indicators i Network Reconstruction". 5th RECOMB Conference on Regulatory Genomics and System Biology, with DREAM challenge, San Francisco, USA, 12-15 novembere 2012
  • A.Barla, M.Filosi, M. Squillario, S. Masecchia, S. Riccadonna, G.Jurman, C. Furlanello. The impact of enrichment variability in pathway profiling, Machine Learning Computational Biology 2011, Granada, December 2011
  • C.Furlanello, M. Roncador, M. Chierici, M. Filosi, R. Visintainer, G.Jurman. Developing pipelines for predictive biomarkers from metagenomics NGS data. International conference on Environmental Omics 2011, Guangzhou, November 2011
  • A.Barla, G.Jurman, R.Visintainer, M. Squillario, M.Filosi, S. Riccadonna and C. Furlanello. A machine learning pipeline for discriminant pathways identification. Computational Intelligence methods for Bioinformatics and Biostatistics 2011, Gargnano sul Garda, June 2011
  • Fontana Francesca, Del Vescovo Valerio, Covello Giuseppina, Bacchi Niccolò, Siva Kavitha, Denti Michela Alessandra.

    Mechanisms of post-trascriptional regulation of gene expression in dementias. II Neuroscience meeting, Cavalese, 19-22 January 2011

  • Gerog J. Weingart, Bruno Fedrizzi, Silvia Carlin, Manoj Ghaste, Urska Vhrovsek, Pietro Franceschi, Matthias Scholz, Ron Wehrens, Fulvio Mattivi, "Establishing an GC-MS based metabolomics platform". 36th International Symposium on Capillary Chromatography

  • M. Lion, A. Bisio, V. De Sanctis, Y. Ciribilli, T. Tebaldi, D. Menendez, M. A. Resnick, A. Inga, "Transcriptional cooperation between p53 and estrogen receptors in a breast cancer model".
  •  
  • Ciribilli Y, Lion M., Bisio A., De Sanctis V., Inga A. "Transcriptional and post-transcriptional control of the FLT1gene by p53 and estrogen receptor". RNA Dynamics Workshop, Ein Gedi, Israel, 15-18 November 2010
  • Bisio A., Ciribilli Y., Del Vescovo V., De Sanctis V., Tonelli C., Lion M., Jegga A.G., Denti M.A., Inga A. "miRNA-based, p53 dependent post-transcriptional circuits: mechanisms, targets and inter-individual variation".

  • Mattia Lion, Yari Ciribilli, Alessandra Bisio, Paola Monti, Virginia Andreotti, Gilberto Fronza, Paola Menichini, Michael A. Resnick and Alberto Inga "p53 Transactivation and the Impact of Mutations, Cofactors and Small Molecules Using a Simplified Yeast-based Screening System". 5th Mutant p53 Workshop, Ariccia-Rome, Italy, 22-25 May 2011

  • Mattia Lion, Alessandra Bisio, Veronica De Sanctis, Yari Ciribilli and Alberto Inga "p53 and estrogen receptors can interact in a synergistic transcriptional cooperation". The 3rd EMBO Meeting, Wien, 10-13 September 2011

  • M. Marchioretto, V. Antonini, L. Lunelli, R. Dallapiccola, T. Praper, G. Anderluh, M. Dalla Serra, "Membrane composition affects pore structure of two cholesterol-dependent cytolysins". 2nd EBSA Biophysics Course, Bordeaux-Lacanau, 24-29 June, 2012

  • M. Marchioretto, V. Antonini, L. Lunelli, R. Dallapiccola, T. Praper, G. Anderluh, M. Dalla Serra, "Listeriolysin O pore-forming abilities on lipid membranes", XXI Congresso Nazional SIBPA, Ferrara, 17-20 settembre 2012

  • M. Marchioretto, V. Antonini, L. Lunelli, R. Dallapiccola, T. Praper, G. Anderluh, M. Dalla Serra, "Membrane composition effects on pore-forming ability of two cholesterol-dependent cytolysins", 8th EBSA European Biophysics Congress, Budapest, Hungary, 23-27 August, 2011

  • V. Antonini, M. Marchioretto, T. Praper, A. Bavdek, G. Anderluh, M. Dalla Serra. "Planar lipid membranes investigation of listeriolysin pore forming ability".
  • L. Marocchi, L. Lunelli, C. Pederzolli, G. Viero, A. Quattrone. "Polysomes interaction with functionalized surfaces".
  • L. Marocchi, L. Lunelli, G. Viero, F. Piras, N. Arseni, A. Provenzali, C. Pederzolli, A.Quattrone. "Polysomes interaction with Self-Assembled Monolayers".
  • Moro A., Di Leva F., Macchi P. "Functional characterization of the RNA binding protein Raly". mRNA Fate 2012, Riva del Garda (Italy), 23-26 May, 2012.
  • Muppirisetty SH., Vaggi F., Inga A., Csikasz-Nagy A., "Revealing the regulation of p53 induced transcription by parameter estimation on p53 induction time-course experiments". 12th International Conference on Systems Biology, Heidelberg/Mannheim August 28 to September 1, 2011

  • Muppirisetty SH, Vaggi F, Ciribilli Y, Inga A, Csikasz-Nagy A, "Analysis of p53 transactivation on different Response Elements", 8th European conference on Mathematical and Theoretical Biology, Krakow Poland, June 28-July 2, 2011

  • Narduzzi Luca, Arapitsas Panagiotis, Della Corte Anna, Angeli Andrea, and Mattivi Fulvio, "Hilic LC-MS:from targeted to untargeted", Workshop on Holistic analytical technologies for biomedical food and plant sciences, Athens, Greece, 9-11 November 2012

  • Alessandro Poli, Andrea Defant, Graziano Guella and Ines Mancini. "DNA interaction with antitumoral molecules: a study by UV- spectroscopy, circular dichroism and docking calculations". XII International Workshop on Complex Systems, Andalo-Trento, Italy, 15-18 March 2010

  • Marina Scarpa, Elena Froner, Paolo Bettotti, Nikola Prtljaga, Eveline Rigo, Silvia Larcheri, Lorenzo Pavesi, Laura Pasquardini, Lorenzo Lunelli, Cristina Potrich, Prashant Pradhan, Cecilia Pederzolli, Adelio Rigo. Nanostructured silicon-based systems for biomedical applications. Nanoforum, Rome, 14-15 September 2011

  • Covello G., Siva K., Denti M.A.,"Antisense RNA-induced Exon-skipping for the gene therapy of frontotemporal dementia and parkinsonism associated with chromosome 17 (FTDP-17)", Abstracts of the 22nd IUBMB & 37th FEBS congress, Seville, Spain, September 4-9, 2012. Published

  • Covello Giuseppina, Siva Kavitha, Bacchi Niccolò, Fontana Francesca, Del Vescovo Valerio, Marchesi Elena, Mari Lara, Perrone Daniela, Denti Michela Alessandra. Antisense RNA-induced Exon-skipping for the gene therapy of frontotemporal dementia and parkinsonism associated with chromosome 17 (FTDP-17). XVI Convention Scientifica Telethon, Riva del Garda, 7-9 March, 2011

  • Wei Sun, Tania Incitti, Claudio Migliaresi, Alessandro Quattrone, Simona Casarosa, Antonella Motta, "Differentiation of embryonic stem cells can be influenced by different processes of Gelatin/Silk Fibroin hydrogel", Stem cells conferences 2012

  • Sabrina Tamburini, Annalisa Ballarini, Giovanna Ferrentino, Olivier Jousson, Paola Foladori, Sara Spilimbergo, "Evaluation of cellular viability of food-borne bacterial pathogens after supercritical CO2 treatment", FEMS 2011. 4th Congress of European Microbiologist. Geneva, Switzerland, June 26-30 2011

  • Sabrina Tamburini, Paola Foladori, Laura Bruni, "Flow cytometry as a rapid tool to assess toxic effects on activated sludge in wastewater treatment plants", FEMS 2011. 4th Congress of European Microbiologist. Geneva, Switzerland, June 26-30 2011

  • Sabrina Tamburini, Annalisa Ballarini, Giovanna Ferrentino, Olivier Jousson, Paola Foladori, Sara Spilimbergo,"Supercritical CO2 treatment induces membrane permeabilization in food-borne bacterial pathogens", SIMGBM 29th National meeting Pisa, Centro Congressi CNR, September 21-23, 2011

  • S. Tamburini, P. Foladori, L. Bruni, V. Menapace, "Effects of ozonation on permeabilisation and disruption of bacteria in activated sludge evaluated by flow cytometry", SIMGBM 29th National meeting Pisa, Centro Congressi CNR, September 21-23, 2011

  • S. Tamburini, P. Foladori, L. Bruni, "Application of flow cytometry for the rapid quantification of viable bacteria and biomass in wastewaster and activated sludge", 15th Cytometry annual conference, Paris 26-28 October 2011

  • Foladori P., Tamburini S., Bruni L. "Effect of sludge reduction techniques causing cell-lysis on bacteria viability and death evaluated by flow cytometry". The Water Research Conference, 11-14 April 2010, Marriott Lisbon, Portugal.
  • Foladori P., Bruni L., Tamburini S., Ziglio G. "Direct Quantification of bacterial biomass in influent, effluent and activated sludge of wastewater treatment plants by using flow cytometry". Bertinoro Meeting di Microbiologia Ambientale (BMMA 2010), Bertinoro (Forlì-Cesena) 21-22 maggio 2010.
  • Paola Torre, Sheref S. Mansy “Building division machinery for the synthesis of cell-like systems". Chemical Synthetic and Systems Biology: New Directions of Biochemistry in the 21st Century, Snowbird, UT, October 12-16, 2011

Contacts

Doctoral School in Biomolecular Sciences
via Sommarive, 14 I - 38123 Povo - Trento Italy
tel. +39 0461 285302