Papers

sorted by type

With PDF's for your personal use.
Papers with * have alphabetical author order.
Names with * contributed equally.
Names with # share senior co-authorship.

2016

  • Development and validation of a whole-exome sequencing test for simultaneous detection of point mutations, indels and copy-number alterations for precision cancer car.
    Hanna Rennert, Ken Eng, Tuo Zhang, Adrian Tan, Jenny Xiang, Alessandro Romanel, Rob Kim, Wayne Tam, Yen-Chun Liu, Bhavneet Bhinder, Joanna Cytra, Himisha Beltran, Brian Robinson, Juan Miguel Mosquera, Helen Fernandes, Francesca Demichelis, Andrea Sboner, Michael Kluk, Mark A. Rubin#, Olivier Elemento#.
  • NPJ Genomic Medicine, 1:16019, 2016. [doi]

2015

  • Plasma AR and abiraterone-resistant prostate cancer.
    Alessandro Romanel*, Delila Gasi Tandefelt*, Vincenza Conteduca, Anuradha Jayaram, Nicola Casiraghi, Daniel Wetterskog, Samanta Salvi, Dino Amadori, Zafeiris Zafeiriou, Pasquale Rescigno, Diletta Bianchini, Giorgia Gurioli, Valentina Casadio, Suzanne Carreira, Jane Goodall, Anna Wingate, Roberta Ferraldeschi, Nina Tunariu, Penny Flohr, Ugo De Giorgi, Johann S. de Bono, Francesca Demichelis#, Gerhardt Attard#.
  • Science Translational Medicine 7, 312re10, 2015[doi] [focus]
  • Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response.
    Himisha Beltran, Kenneth Eng, Juan Miguel Mosquera, Alexandros Sigaras, Alessandro Romanel, Hanna Rennert, Myriam Kossai, Chantal Pauli, Bishoy Faltas, Jacqueline Fontugne, Kyung Park, Jason Banfelder, Davide Prandi, Neel Madhukar, Tuo Zhang, Jessica Padilla, Noah Greco, Terra J. McNary, Erick Herrscher, David Wilkes, Theresa Y. MacDonald, Hui Xue, Vladimir Vacic, Anne-Katrin Emde, Dayna Oschwald, Adrian Y. Tan, Zhengming Chen, Colin Collins, Martin E. Gleave, Yuzhuo Wang, Dimple Chakravarty, PMarc Schiffman, Robert Kim, Fabien Campagne, Brian D. Robinson, David M. Nanus, Scott T. Tagawa, Jenny Z. Xiang, Agata Smogorzewska, Francesca Demichelis, David S. Rickman, Andrea Sboner, Olivier Elemento, Mark A. Rubin.
  • Jama Oncology 1(4):466, 2015[doi]
  • *On the impact of discreteness and abstractions on modelling noise in gene regulatory networks.
    Chiara Bodei, Luca Bortolussi, Davide Chiarugi, Maria Luisa Guerriero, Alberto Policriti, Alessandro Romanel.
  • Computational Biology and Chemestry 56:98-108, 2015[doi]
  • ASEQ: fast allele-specific studies from next-generation sequencing data.
    Alessandro Romanel, Sara Lago, Davide Prandi, Andrea Sboner, Francesca Demichelis.
  • BMC Medical Genomics 8(1):9, 2015[doi]
  • In-silico identification and functional validation of allele-dependent AR enhancers.
    Sonia Garritano*, Alessandro Romanel*, Yari Ciribilli*, Alessandra Bisio, Antoneta Gavoci, Alberto Inga#, Francesca Demichelis#.
  • Oncotarget 6(7):4816-4828, 2015[url]

2014

  • Tumor clone dynamics in lethal prostate cancer.
    Suzanne Carreira*, Alessandro Romanel*, Jane Goodall*, Emily Grist, Roberta Ferraldeschi, Susana Miranda, Davide Prandi, David Lorente, Jean-Sebastien Frenel,Carmel Pezaro, Aurelius Omlin, Daniel Nava Rodrigues, Penelope Flohr, Nina Tunariu, Johann S de Bono, Francesca Demichelis#, Gerhardt Attard#.
  • Science Translational Medicine 6, 254ra125, 2014. [doi] [focus]
  • Unraveling the clonal hierarchy of somatic genomic aberrations.
    Davide Prandi, Sylvan C Baca, Alessandro Romanel, Christopher E Barbieri, Juan Miguel Mosquera, Jacqueline Fontugne, Himisha Beltran, Andrea Sboner, Levi A Garraway, Mark A Rubin, Francesca Demichelis.
  • Genome Biology 15:439, 2014[doi]
  • *The Spider Calculus: Computing in Active Graphs.
    Benjamin C Pierce, Alessandro Romanel, Daniel Wagner.
  • Essays for the Luca Cardelli Fest, MSR-TR-2014-104, 2014[url]

2013

  • Punctuated Evolution of Prostate Cancer Genomes.
    Sylvan C. Baca, Davide Prandi, Michael S. Lawrence, Juan Miguel Mosquera, Alessandro Romanel, Yotam Drier, Kyung Park, Naoki Kitabayashi, Theresa Y. MacDonald, Mahmoud Ghandi, Eliezer Van Allen, Gregory V. Kryukov, Andrea Sboner, Jean-Philippe Theurillat, T. David Soong, Elizabeth Nickerson, Daniel Auclair, Ashutosh Tewari, Himisha Beltran, Robert C. Onofrio, Gunther Boysen, Candace Guiducci, Christopher E. Barbieri, Kristian Cibulskis, Andrey Sivachenko, Scott L. Carter, Gordon Saksena, Douglas Voet, Alex H. Ramos, Wendy Winckler, Michelle Cipicchio, Kristin Ardlie, Philip W. Kantoff, Michael F. Berger, Stacey B. Gabriel, Todd R. Golub, Matthew Meyerson, Eric S. Lander, Olivier Elemento, Gad Getz, Francesca Demichelis#, Mark A. Rubin#, Levi A. Garraway#.
    Cell 153(3):666-677, 2013. [pubmed] [doi] [highlight in Nature Reviews Cancer]
  • Distinct ERG rearrangement prevalence in prostate cancer: higher frequency in young age and in low PSA prostate cancer.
  • G Schaefer, J-M Mosquera, R Ramoner, K Park, A Romanel, E Steiner, W Horninger, J Bektic, M ladurner-Rennau, MA Rubin, F Demichelis#, H Klocker#.
    Prostate Cancer and Prostatic Disease 16:132-138, 2013. [pubmed[doi] [highlight in Nature Reviews Urology]

2012

  • Transcriptional regulation is a major controller of cell cycle transition dynamics.
    Alessandro Romanel, Lars Juhl Jensen, Luca Cardelli, Attila Csikász-Nagy.
    PLoS ONE 7(1) e29716, 2012. [pubmed] [doi] [pdf[supp] 
2011
  • Evolving Programs to Simulate Molecular Evolution
    Alessandro Romanel.
    Newsletter IEEE TCSIM, issue 9
    , June 2011. [url
2010
  • Estimating the divisibility of complex biological networks by sparseness indices
    Tommaso Mazza, Alessandro Romanel, Ferenc Jordán.
    Briefings in Bioinformatics
    11(3):364-374, © Oxford Journals, 2010. [pubmed] [doi] [bib] [pdf]
  • Self-assembly processes with cooperativity. [bib] [pdf]
    Alessandro Romanel.
    In Proceedings of 9th Workshop on Process Algebra and Stochastically Timed Activities (PASTA)
    , 2010.
  • *Programming Biology in BlenX. [doi] [bib] [pdf]
    Lorenzo Dematté, Roberto Larcher, Alida Palmisano, Corrado Priami, Alessandro Romanel.
    In Systems Biology for Signaling Networks 1:777-820, Ed. Sangdun Choi, © Springer, 2010.
  • *Modelling self-assembly in BlenX. [doi] [bib] [pdf]
    Roberto Larcher, Corrado Priami, Alessandro Romanel.
    Transactions on Computational Systems Biology XII
    , LNCS 5945:163-198, © Springer, 2010.
  • Dynamic Biological Modelling: a language-based approach.
    Alessandro Romanel.

    PhD thesis
    , University of Trento, 2010. [bib] [pdf] [slides]
  • *The Spider Calculus: Computing in Active Graphs. [bib] [pdf]
    Benjamin C. Pierce, Alessandro Romanel, Daniel Wagner.
    January 2010.
  • On the Computational Power of BlenX.
    Alessandro Romanel, Corrado Priami.
    Theoretical Computer Science
    411(2):542-565, © Elsevier, 2010. [doi] [bib] [pdf]
2009
  • Towards a process calculi approach to study the evolution of biological networks. [bib] [pdf]
    Alessandro Romanel.
    In Proceedings of 8th Workshop on Process Algebra and Stochastically Timed Activities (PASTA)
    , 2009.
  • *BlenX Static and Dynamic Semantics. [doi] [bib] [pdf]
    Corrado Priami, Paola Quaglia, Alessandro Romanel.
    In Proceedings of 20th International Conference on Concurrency Theory (CONCUR)
    , LNCS 5710:37-52, © Springer, 2009.
  • *Exploiting non-Markovian Bio-Processes. [doi] [bib] [pdf]
    Ivan Mura, Davide Prandi, Corrado Priami, Alessandro Romanel.
    In Proceedings of 7th Workshop on Quantitative Aspects of Programming Languages (QAPL)
    , ENTCS 253(3):83-98, Elsevier, 2009.
  • *Analyzing various models of Circadian Clock and Cell Cycle coupling. [url] [bib]
    Paolo Ballarini, Attila Csikász-Nagy, Adrien Faure, Roberto Larcher, Paola Lecca, Tommaso Mazza, Ivan Mura, Ferenc Jordán, Alida Palmisano, Alessandro Romanel, Sean Sedwards, Heike Siebert, Sylvain Soliman, Denis Thieffry and Judit Zámborszky.
    Formal Methods in Molecular Biology
    , Dagsthul seminar proceedings 09091, 2009.
2008
  • *Evolving BlenX programs to simulate the evolution of biological networks. [doi] [bib] [pdf]
    Lorenzo Dematté, Corrado Priami, Alessandro Romanel, Orkun Soyer.
    Theoretical Computer Science
    408(1):83-96, © Elsevier, 2008.
  • Varying the level of abstraction in stochastic molecular dynamics models.
    Ivan Mura, Alida Palmisano, Sean Sedwards, Lorenzo Dematté, Alessandro Romanel.
    Poster, International Conference on Systems Biology (ICSB) 2008
    .
  • *The Beta Workbench: a computational tool to study the dynamics of biological systems. [pubmed] [doi] [bib] [pdf]
    Lorenzo Dematté, Corrado Priami, Alessandro Romanel.
    Briefings in Bioinformatics
    9(5):437-449, © Oxford Journals, 2008.
  • *The BlenX Language: A Tutorial. [doi] [bib] [pdf]
    Lorenzo Dematté, Corrado Priami, Alessandro Romanel.
    In SFM 2008, LNCS 5016:313-365, © Springer, 2008.
  • On the Decidability and Complexity of the Structural Congruence for Beta-binders. [doi] [bib] [pdf]
    Alessandro Romanel, Corrado Priami.
    Theoretical Computer Science
    404(1-2):156-169, © Elsevier, 2008.
  • *Modelling and simulation of biological processes in BlenX. [doi] [bib]
    Lorenzo Dematté, Corrado Priami, Alessandro Romanel.
    SIGMETRICS Performance Evaluation Review
    35:32-39, ACM, 2008.
  • *Simulation of non-Markovian processes in BlenX. [pdf]
    Davide Prandi, Corrado Priami, Alessandro Romanel.
    COSBI TR-11-2008.
2007
  • *A Formal and Integrated Framework to Simulate Evolution of Biological Pathways. [doi] [bib]
    Lorenzo Dematté, Corrado Priami, Alessandro Romanel, Orkun Soyer.
    In Proceedings of International Conference on Computational Methods in Systems Biology (CMSB)
    , LNBI 4695:106-120, © Springer, 2007.
  • *BetaWB: modelling and simulating biological processes. [bib] [pdf]
    Lorenzo Dematté, Corrado Priami, Alessandro Romanel.
    In Proceedings of Summer Computer Simulation Conference (SCSC) 2007
    .
  • *Effective Index: A formal measure of drug effects. [bib] [pdf]
    Lorenzo Dematté, Davide Prandi, Corrado Priami, Alessandro Romanel.
    In Proceedings of 2nd Conference Foundations of Systems Biology in Engineering (FOSBE) 2007
    .
  • *Modeling Static Biological Compartments with Beta-binders. [doi] [bib] [pdf]
    Maria Luisa Guerriero, Corrado Priami, Alessandro Romanel.
    In Proceedings of Algebraic Biology, Second International Conference (AB) 2007
    , LNCS 4545:247-261, © Springer-Verlag, 2007.
  • *The Decidability of the Structural Congruence for Beta-binders. [doi] [bib]
    Corrado Priami, Alessandro Romanel.

    In Proceedings of Workshop on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC) 2006
    , ENTCS 171(2):155-170, Elsevier, 2007.
  • *The Beta Workbench. [pdf]
    Lorenzo Dematté, Corrado Priami, Alessandro Romanel.
    COSBI TR-03-2007.
2006
  • Simple Methods for Peak and Valley Detection in Time Series Microarray Data. [doi] [bib] [pdf]
    Andrea Sboner, Alessandro Romanel, Andrea Malossini, Federica Ciocchetta, Francesca Demichelis, Ivano Azzini, Enrico Blanzieri, Rossana Dell'Anna.
    In Methods of Microarray Data Analysis V, © Springer, 2006.
2005
  • A Novel Quality Control Procedure for Gene Expression Time Series.
    Andrea Sboner, Alessandro Romanel, Andrea Malossini, Francesca Demichelis, Federica Ciocchetta, Marco Stenico, Enrico Blanzieri, Rossana Dell'Anna.
    BITS Annual Meeting 2005
    .