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Publications

Here is a list of publications about the activity of the laboratory.

Papers in journals

  • Romano P, Profumo A, Rocco M, Mangerini R, Ferri F, Facchiano A. Geena 2, improved automated analysis of MALDI/TOF mass spectra. BMC Bioinformatics 2016, 17(Suppl 4):61. DOI: doi:10.1186/s12859-016-0911-2 PMID: 26961516
  • Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, et al. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research 44 (D1), D38-D47. DOI: doi:10.1093/nar/gkv1116 PMID: 26538599
  • Boccardo F, Rubagotti A, Nuzzo PV, Argellati F, Savarino G, Romano P, Damonte G, Rocco M, Profumo A. Matrix-assisted laser desorption/ionisation (MALDI) TOF analysis identifies serum Angiotensin II concentrations as a strong predictor of all-cause and breast cancer (Bca)-specific mortality following breast surgery. International Journal of Cancer. 2015, 137(10):2394-2402. Published on-line 15 November 2015. DOI: doi:10.1002/ijc.29609 PMID: 25994113
  • Masseroli M, Mons B, Bongcam-Rudloff E, Ceri S, Kel A, Rechenmann F, Lisacek F, Romano P. Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information. BMC Bioinformatics 2014, 15(Suppl 1):S2 (10 January 2014) DOI: doi:10.1186/1471-2105-15-S1-S2 PMID: 24564249
  • Profumo A, Mangerini R, Rubagotti A, Romano P, Damonte G, Guglielmini P, Facchiano A, Ferri F, Ricci F, Rocco M, Boccardo F. Complement C3f serum levels may predict breast cancer risk in women with gross cystic disease of the breast. Journal of Proteomics 2013, 85:44-52. DOI: doi:10.1016/j.jprot.2013.04.029 PMID: 23639844
  • Romano P, Cannata N. NETTAB 2013: Semantic, social, and mobile applications for bioinformatics and biomedical laboratories. BMC Bioinformatics 2014, 15(Suppl 14):S1 (27 November 2014) DOI: doi:10.1186/1471-2105-15-S14-S1 PMID: 25471662
  • Bellazzi R, Masseroli M, Shawn M, Shabo A, Romano P. Clinical Bioinformatics: challenges and opportunities.
    BMC Bioinformatics 2012, 13(Suppl 14):S1. Published on-line 7 September 2012. DOI: doi:10.1186/1471-2105-13-S14-S1 PMID: 23095472
  • Miele M, Mumot AM, Zappa A, Romano P, Ottaggio L. Hazel and other sources of paclitaxel and related compounds. Phytochemistry Reviews. 2012. Published on-line 23 May 2012. DOI: doi:10.1007/s11101-012-9234-8
  • Zappa A, Splendiani A, Romano P. Towards linked open gene mutations data. BMC Bioinformatics 2012, 13(Suppl 4):S7 DOI: doi:10.1186/1471-2105-13-S4-S7 PMID: 22536974
  • Bolser DM, Chibon P-Y, Palopoli N, Gong S, Jacob D, Dominguez Del Angel V, Swan D, Bassi S, Gonzales V, Suravajhala P, Hwang S, Romano P, Edwards R, Bishop B, Eargle J, Shtatland T, Provart NJ, Clements D, Renfro DP, Bhak D, Bhak J. MetaBase – The wiki-database of biological databases. Nucleic Acids Research, 2011, Advance Access published December 1, 2011. DOI: doi:10.1093/nar/gkr1099 PMID: 22139927
  • Romano P, Giugno R, Pulvirenti A. Tools and collaborative environments for bioinformatics research. Brief Bioinform (2011) first published online October 7, 2011. DOI: doi:10.1093/bib/bbr055 PMID: 21984743
  • Mangerini R, Romano P, Facchiano A, Damonte G, Muselli M, Rocco M, Boccardo F, Profumo A. The application of atmospheric pressure MALDI to the analysis of long-term cryopreserved serum peptidome. Analytical Biochemistry 417 (2011) 174-181. DOI: doi:10.1016/j.ab.2011.06.021 PMID: 21756868
  • Splendiani A, Burger A, Paschke A, Romano P, Marshall MS. Biomedical semantics in the Semantic Web. J Biomed Semantics. 2011 Mar 7;2 Suppl 1:S1. DOI: doi:10.1186/2041-1480-2-S1-S1 PMID: 21388570
  • Zappa A, Miele M, Romano P. IBWS: IST Bioinformatics Web Services. Nucleic Acids Research (2010) 38 (suppl 2): W712-W718. DOI: doi:10.1093/nar/gkq416 PMID: 20484374
  • Milanesi L, Romano P, Castellani G, Remondini D, Liò P. Trends in modeling Biomedical Complex Systems. BMC Bioinformatics 2009, 10(Suppl 12):I1. DOI: doi:10.1186/1471-2105-10-S12-I1 PMID: 19828068
  • Corradi L, Mirisola V, Porro I, Torterolo L, Fato M, Romano P, Pfeffer U. Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data. BMC Bioinformatics 2009, 10(Suppl 12):S10. DOI: doi:10.1186/1471-2105-10-S12-S10 PMID: 19828070
  • Burger A, Romano P, Paschke A, Splendiani A. Semantic Web Applications and Tools for Life Sciences, 2008 (Preface). BMC Bioinformatics 2009, 10(Suppl 10):S1. DOI: doi:10.1186/1471-2105-10-S10-S1 PMID: 19796393
  • P. Romano, A. Manniello, O. Aresu, M. Armento, M. Cesaro, B. Parodi. Cell Line Data Base: structure and recent improvements towards molecular authentication of human cell lines. Nucleic Acids Research 2009 37(Database issue):D925-D932. DOI: doi:10.1093/nar/gkn730 PMID: 18927105
  • N. Cannata, M. Schröder, R. Marangoni, P. Romano. A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications. BMC Bioinformatics, 2008 9(Suppl 4):S1. DOI: doi:10.1186/1471-2105-9-S4-S1 PMID: 18460170
  • P. Romano, D. Marra. SWS: accessing SRS sites contents through Web Services. BMC Bioinformatics, 2008 9(Suppl 2):S15. DOI: doi:10.1186/1471-2105-9-S2-S15 PMID: 18387203
  • P. Romano. Automation of in-silico data analysis processes through workflow management systems. Briefings in Bioinformatics, 2008 9(1):57-68. DOI: doi:10.1093/bib/bbm056 PMID: 18056132
  • E. Bartocci, D. Cacciagrano, N. Cannata, F. Corradini, Merelli, L. Milanesi, and P. Romano. An Agent-based Multilayer Architecture for Bioinformatics Grids. IEEE Transactions on NanoBioscience (IEEE-TNB), 2007, 6(2):142-148. DOI: doi:10.1109/TNB.2007.897492
  • G. Armano, V. Breton, L. Milanesi, P. Romano. Special Section on GRID, Web Services, Software Agents, and Ontology Applications for Life Sciences (Guest Editorial). IEEE Transactions on NanoBioscience (IEEE-TNB), 2007, 6(2):101-103. DOI: doi:10.1109/TNB.2007.897434
  • Romano P, Bartocci E, Bertolini G, De Paoli F, Marra D, Mauri G, Merelli E, Milanesi L. Biowep: a workflow enactment portal for bioinformatics applications. BMC Bioinformatics 2007, 8(Suppl 1):S19. Full free text on BioMed Central PMID: 17430563
  • P. Romano, G. Bertolini, F. De Paoli, M. Fattore, D. Marra, G. Mauri, E. Merelli, I. Porro, S. Scaglione and L. Milanesi. Network integration of data and analysis of oncology interest. Journal of Integrative Bioinformatics, 0021, 2006. Online Journal: http://journal.imbio.de/index.php?paper_id=21
  • Romano, P., Marra, D., and Milanesi, L. Web services and workflow management for biological resources. BMC Bioinformatics 2005, 6(Suppl 4):S24. PMID: 16351751
  • Romano, P., Dawyndt, P., Piersigilli, F., and Swings, J. Improving interoperability between microbial information and sequence databases. BMC Bioinformatics 2005, 6(Suppl 4):S23. PMID: 16351750
  • Romano P, Kracht M, Manniello MA, Stehehuis G, Fritze D. The role of informatics in the coordinated management of biological resources collections. Appl Bioinformatics. 2005;4(3):175-86. PMID: 16231959
  • Romano, P., Aresu, O., Manniello, M.A., Parodi, B. Interoperability of CABRI services and biochemical pathways databases. Comp Funct Genom 2004; 5:169-172. DOI: doi:10.1002/cfg.376 Abstract on-line
  • P. Arrigo, P. Romano, P. Scartezzini. AgeWa: an integrated approach for antisense experiment design. IEEE Transactions on NanoBioscience, 1(4):167-171, December 2002.
  • Campi M.G., Romano P., Milanesi L., Marra D., Manniello M.A., Iannotta B., Rondanina G., Grasso E., Ruzzon T. and Santi L. Molecular Probe Data Base (MPDB). Nucleic Acids Research, 26:1: 145-147, 1998. PMID: 147247 [Summary] [Page Browse] [PDF][Links]
  • Aresu O., Romano P., Parodi B., Iannotta B., Rondanina G., Ruzzon T., Santi L. Interlab Project Databases: A Support for Biotechnological Research. Cancer Detection and Prevention, 17(2):355, 1993.

Other publications

  • Romano P, Milanesi L. Complex Search, Ranks, and Biological Discovery: A User’s Perspective. In “Search Computing Trends and Developments”. Ceri S, Brambilla M (eds). Lecture Notes in Computer Science, 2011, Volume 6585/2011, 226-235. DOI: doi:10.1007/978-3-642-19668-3_21
  • P. Romano, A. Splendiani. Applications of Semantic Web methodologies and techniques to biology and bioinformatics. Reasoning Web 2008, Springer Lecture Notes in Computer Sciences LNCS 5224, pp. 200-239, 2008, Springer Verlag Berlin Heidelberg. DOI: doi:10.1007/978-3-540-85658-0_6
  • Marra, D. and Romano, P. Integrating mutation data of the TP53 human gene in the bioinformatics network environment. Proc. First International Conference on Bioinformatics Research and Development BIRD ’07, March 12-14, 2007, Berlin. Springer Lecture Notes in Bioinformatics LNBI 4414, pp. 453-463, 2007, Springer Verlag Berlin Heidelberg 2007. DOI: doi:10.1007/978-3-540-71233-6_35
  • Romano P, Bertolini G, De Paoli F, Fattore M, Marra D, Mauri G, Merelli E, Porro I, Scaglione S, Milanesi L. Network integration of data and analysis of oncology interest. In Integrative Bioinformatics Yearbook 2005. Edited by R. Hofestadt, Aachen: Shaker Verlag; 2006: 111-121. ISBN: 3-8322-5268-1
  • Facchiano, A., Romano, P., Rossi, E. NETTAB:
    Bioinformatica per Microarray
    (in italian). Notizie dal CINECA, 48:16-17, 2003. DOI: doi:10.1388/notizie-48-06
  • Romano P. and Merelli E. NETTAB 2002
    workshop on “Agents in Bioinformatics
    “, AgentLink Newsletter, 11:19-20, November 2002.
  • Romano P. Network tools and services for biomedical research. Proceedings of the 1st Italian Seminar on Bioinformatics. Camerino, June 9-11, 1994.
  • Romano P., Aresu O., Iannotta B., Manniello A., Parodi B., Rondanina G., Ruzzon T. Interlab Project Databases: an effort towards the needs of a wider body of unskilled users. Binary, 5:66-72, 1993.
  • Romano P., Iannotta B., Rondanina G., Ruzzon T. The Interlab Project Network for Biomedical Research. Bioinformatics, 1(3):4-11, 1992.